I just rode about 45 miles this morning with a 48 16 single speed, T shirt, regular shorts, and regular shoes. Will clipless pedals, clipless shoes, cycling shorts, jersey and multi gearing make a difference in terms of speed. I did about 15 mph avg for the ride, how much difference would having all that equipment make? Will my speed go up with the same effort or will it stay the same? I found climbing up hills very tough, at 8% grade I was pedaling at 25 cadence.

The gears will help on the climbs, but the shorts, jersey and pedals probably won't make a difference. But you might be more comfortable.

I was quite uncomfortable on my saddle, while riding I was constantly being thrown up and down from my saddle.

its generally not a good idea to bike naked, so id stick with the clothes.

The clothes will probably be the biggest gain, simply by not catching the wind. Pedals will be the next best, by allowing you to apply more torque when the SS is bogging down, and to spin much faster without your feet flying off.

Combined with that, I would probably lower the gear a bit, especially if you have some modest hills. The cleats will make that safer. For flat ground, my SS has 44-16, which is a bit much for headwinds, but I enjoy the workout and can pedal fairly well at 200rpm on the downwind side.

A SS is quite fast with a good gear selection, even if never optimum. I can't tell from my numbers alone if I am riding SS or gears on the flats, even with moderate winds. But any real hills; I always take a bike with gears.

If you gained 1mph from all the changes, that would be a pretty optimistic outcome, but comfort would be way better. There are endless optimization so to be had, but gains are very incremental.

If you only make one change, I think gears will help you a lot to deal with the hills and leave you with more energy for the flats!

That sounds more like the bicycle isn't set up correctly and/or you aren't in the right gear on the bicycle. Shift!

No.
As you have indicated in your profile your machine is a Fixed Gear running 79 gear inches while climbing an 8% grade pedaling at 25 cadence.
This is completely normal.

The Illusion of more positive foot retention, comfortable/appropriate clothing and/or variable gearing for terrain/fitness levels is Cycling Maya.

The Eightfold Path of Pseudo-Zen Fixed Gear Cycling reveals:

The Right View: Doing a shoulder check before turning left in traffic.
The Right Thought: No thought at all.
The Right Speech: "Yo, Hey Dude!"
The Right Action: An uncontrolled skid for no reason.
The Right Livelihood: Waiter
The Right Effort: That 8% grade pedaling at 25 cadence.
The Right Mindfulness: "Where's my keys?"
The Right Concentration: "I don't have any brakes coming Down this 8% grade!"

Karmic-ly yours,

-Bandera

If you bought all that gear you would be faster because your wallet would be much lighter.

Otherwise you wouldn't really notice any difference.

Cycling shorts with a chamois makes sense most for road riders who don't move a lot on the saddle---they are most prone to chafing. An SS rider who is always up and down is less likely to develop saddle sores.

The jersey won't catch as much sweat and will pass more air, but unless you are riding in the tropics the effect is minimal. I find jerseys a little bit more comfortable on really hot humid days but I (and the rest of the world) rode in cotton T-shirts for decades with no adverse effects.

The biggest gain with cycling shoes is the stiffer sole. There might be (depending on whose Internet post you believe) some tiny percentage gained on the upstroke with clips but not very much by even the most optimistic estimates.

On the other hand, your feet will not cramp so much after you ride, and your calves hopefully won't hurt quite so much, as cycling shoes have very stiff soles.

A reasonable low-cost alternative here is the rat-trap approach, with the traditional toe-clips and straps---you can gauge for yourself how much faster you go while attached to the pedals, and decide if the several hundred-dollar investment in pedals and shoes is worth it.

Gearing will make a huge boost in efficiency ... not necessarily in pleasure.Some folks love pounding it out on single-speeds ... and power to them. But unquestionably you will go further and faster on a geared bike---IF you use the gears properly.

However, the cost of adding gears to an SS frame is Way beyond all that other gear ... you would be best off buying a whole new bike---(which is pretty much the answer to all questions on BF, as a poster pointed out.)

I think it's been said well but I doubt you'd see any meaningfull gains in speed with those clothing upgrades, but perhaps some in comfort. Human minds plays tricks on us though, and sometimes doing this does make us faster, but its just a temporary mind trick. First time I put on a full bike color matching kit I felt fast, and went fast. But now-a-days I ride more like you and don't have a problem. A $10 (or less) pair of poly athletic underwear prevent most any chaffing and can be worn under any shorts. I have no problem riding barefoot on platform pedals either, done century ride and multi-day tour approaching century distance daily without needing any of this stuff. But I am not breaking any speed records though. I do prefer the bike clothing on a really hot sweaty ride though, as they mitigate sweat a little better and it doesn't show, my regular shorts I typically wear are actually mostly cotton and really show the sweat.

If I were in your shoes as they say, I'd skip the accessory gear and focus on gears [literally] if you're on a SS and in the hills I would think having gears would be the single biggest gain in efficiency, followed next by lighter wheels (unless your are already light).

You might have missed he said that he was on a single speed, 48-16.

I'll differ here from what seems to be a developing consensus: tight non-flapping clothing does make a difference. Even at 15 or 16 mph. How much we "notice" depends on how fast we're trying to go, how close to our limit that is.

What I mean is, if you're riding at some moderate effort you probably can't tell. I don't think that anyone can tell the difference between 55% threshold and 60% at some given speed, unless they train consistently with power. But at 95% or 100% threshold, that 1/2 mph difference is pretty easy to spot. It doesn't matter if the FTP limit happens to be 15 mph or 25 mph, you can tell when you've gained or lost that fractional mph speed. Clothing that flaps is a large drag.

Foot retention on the other hand, I think makes literally zero difference in speed. People appreciate it for other reasons. (If OP has a fixed gear as in his profile, foot retention is advisable. If a SS as per his post, it's not that important in my experience)

I think I've already discussed gearing with OP in his other thread so I won't comment here.

After a 30+ mile ride I do start to get the feeling on the saddle area as if every hair is being pulled there even though I dont have much considerable amount of hair. I come home feeling like my bottom is all irritated, Is that normal for all cyclists or are there any solutions to that?

Not normal at all.
Padded cycling shorts?

or hammock leather saddle (Brooks, etc.) - canvas shorts without any padding is fine

Your speed is average and normal for a newbie riding a SS...Your cadence will never be the same on a SS bike as on a multi geared bike. It's perfectly normal for cadence to be very slow when climbing hills on a SS...Hill climbing on SS or FG has a lot to do with a technique, the more your practice the better you become.
Foot retention such as clipless or toeclips with straps will make climbing a little easier and make pedalling more efficient. Padded shorts makes your ride more comfortable. Just enjoy your ride and stop obsessing too much about speed.

Just reglar shorts I would wear any day.

I use a full carbon fiber saddle and find it way more comfortable than all the stock saddles I have owned. I weigh only 130 lbs so I shouldn't have a problem with these saddles right?

If you want to go fast, get a bike with gears, its that simple.

A single speed is a bike thats in the wrong gear 95% of the time and if its a fixed gear, you can't go fast around corners without a corner strike.

Besides, fixies are sooo 2008. Hipsters have long given up the fixie.

Track Races they being a bag with extra Cogs and chainrings to tailor the gear to the Day's needs.

gears. which probably means a new bike. i've read conflicting reports on clipless pedals so have never tried them. but for my primarily urban riding they don't make much sense anyways. but some say they will make you 33% more efficient. Others say the benefits are minimal at best.

Air Resistance is the enemy of speed . 2x speed meets 4x resistance..

Battle Mountain NV speed competitions they all are laying down, in fish like shaped Recumbents

Flying 200M speed is over 80mph.

I know the feeling. Happens to me when I ride wearing regular shorts and underwear. (For whatever it's worth, it seems to be less of a problem with briefs than boxers or even boxer briefs.)

When wearing cycling shorts, on the other hand, it's not a problem at all.

Clipless shoes and pedals are mostly a matter of confidence due to not having to think about foot contact. They'll generally offer close to zero actual performance improvement, and can potentially even slow you down if you're not careful about having a good pedal stroke, as they enable bad habits. I like them and use them on all my road bikes, but I wouldn't say they're critical to performance.

Cycling clothing does matter relative to flappy stuff, in terms of aerodynamics. Won't make an astronomical difference at 15mph, but it becomes more significant at higher speeds.
You mentioned that you've been chafing. Most cycling shorts include a chamois pad, which wicks and doesn't bunch up. In addition to the chamois pad, many cyclists also use chamois cream for lubrication. Makers of chamois cream even sell small packets that people carry on rides in case they need to re-apply.
Cycling jerseys also usually have 3 easily-reachable pockets in back, which is nice.

Unless you ride at constant-effort on flat ground with no wind and have no stops, multi-speed gearing is a huge difference. Too low an RPM, and our legs are very inefficient when trying to drive huge force into a pedal that's barely moving. Too high an RPM, and we're wasting lots of energy just moving our legs in circles.

Maybe your saddle is slightly too high?

Sometimes I wear cargo shorts (I know.... they do catch the wind). When I do, I make sure to wear something like UnderArmor underwear briefs underneath. The synthetic underwear has to be tight enough not to move around ON YOU. It also should be wicking, so as not to absorb and hold moisture, which can also cause problems.

Don't get on your bike with only your normal cotton shorts, unless it is for something like a short or leisurely paced fun ride.
edit: Your undershorts should be akin to a second skin, without being uncomfortably restrictive.

Gears will make significant difference in your ability to maintain a cadence of your preference which will hopefully allow you to more effectively create more power.

Clothing absolutely makes a huge difference. Probably the most significant upgrade you could make over your current setup in regards to buying speed would be a skinsuit. Since a skinsuit isn't too practical, regular cycling shorts (bibs will likely be your best bet, there) with a small, tight-fitting jersey will still be a tremendous upgrade over what you're currently wearing. Comfort factor will be a huge boon, too.