Bike Forums - new-2-me bike, some fit questions

I was riding a old Walmart type mountain bike for exercise. I decided that there wasn't much sense in driving to and from work every day just to come home and ride for an hour. So I decided to join the bike commuter ranks. As part of that, I needed a better bike (chain/derailer/cog issues, along with a few other things on the Wmart bike) & wanted to get into a bit of a lower riding position, since there always seemed to be a headwind.

I bought a used mid '90s Bianchi Boardwalk & just haven't been able to get real comfortable on it. I'm currently riding about 100 miles a week & have been riding about 70-90 miles for the prior 2 months. I have some noob style questions I'm hoping that you can help me with.

The bike frame is larger than the mtn bike, I have about 1-1.5" of stand-over clearance. I figured this was a bit tight, but most likely ok since it is only for road use. The headtube is also a bit longer (about 1").

I've played with saddle position (height, angle and forward/aft), I've swapped in a couple of stems (about 1" difference in length) & added some bar ends to the flat handle bar (I prefer to ride on them rather than back on the bar).

I've got the saddle about as high as I can get it... another 1/4"-3/8" higher & I either need to rock my hips or lift my foot off the pedals. The saddle and handlebars are almost dead even in height.

On to my problems:
1) I'm experiencing some numbness in the perineum that I didn't have on the other bike (I'm male). If I drop the nose of the saddle a bit, I seem to be too far forward/need to brace with my arms, if I try raising it, the numbness gets worse/painful. Currently the angle is pretty much level with the ground, which seems to be the best. I've tried a couple of different saddles from bikes around the house including a harder nosed Schwinn, but none seem to make the numbness go away. It only takes about 5 miles before it kicks in.

2) I feel kind of "hunched" when I've got the shorter stem, which doesn't seem to make much sense, since it's still about 3/4" longer from the handlebars to the saddle than the MTB was. It even feels a bit constrained when I reach forward to the bard ends. So I'm currently running with the longer stem which puts me about 1 3/4" longer (saddle to handlebars) than what I was running. I'm not sure if this is imagination or reality, but it's the way that I feel.

3) If I try to up my cadence (which I 'm trying to work on), I feel my upper thighs hitting my belly (5'9"/175 lbs). When I have my seat raised any higher, instead of thighs hitting the belly I get either hip rocking or feet getting very light on the petals at the bottom. This only seems to be a bother when I try to raise my cadence as I don't notice it at my current cadence (likely someplace around 65).

4) I can't seem to stand up on the bike. I've never had this problem before with any bike. When I stand, it feels like I'm leaning too far forward & my hands are behind my shoulders & my thighs are almost into the handlebars. If I try to force myself backwards, I bump into the seat. The only way to stand & climb seems to be to let the bike sway from side to side, but I don’t feel like I get any additional force/pull up on the bars when I do this, with my hands seemingly behind my shoulders.

I noted that if I push my foot down to the "bottom" of the stroke & lock my knee (allowing my heal to drop slightly below the pedal/ball of my foot) my pedal is at the 7-7:30 o'clock position rather than the 6-6:30 o'clock position I would expect. Is this normal?

Are all of these things inter-related & are there solutions? For example, I’m thinking the foot being light on the bottom of the stroke might be solved with a clip pedal, which might let me raise the seat 3/8” which might…

Or is it simply the way that a hybrid bike is (ie the weird leaning forward feeling when I try to stand) since my previous bike experience was all either mtn bikes, kid bikes or “10 speeds”?

Thank you for your advice.
Why2not