There's loads that goes into a good fit, and it can be slightly counter-intuitive. I don't know how much you know, so excuse me ahead of time if I say things you already know.
To begin with, as for saddle position...this is the most important aspect of bike-fitting. Your saddle really has one place it should be, depending on your preference. The term used is KOPS (Knee Over Pedal Spindle). You can google this, but a quick description is that the bottom of your kneecap should line up with the spindle of your pedal with your crank at 3:00 pm...you need a plum bob to really be accurate.
Of course, this is tricky, because time trial bikes and triathalon bikes will have the rider more in front of pedal spindle, and hill climb bikes (like MTBs) will be a bit behind. You have to do some experimentation to find out where you want to be, and it sounds like you've done some.
Most road riders, recreational and commuting, prefer to be a bit behind the pedal spindle with their knee. It makes for a more comfortable spin, and it allows them to more effectively use the bio-dynamics to keep weight off of their hands and arms.
The second thing I worry about is saddle height. The majority of riders I see with bad fits have their seats too high. It seems like most people have heard the dogma about their saddle being high enough that their leg is almost extended at the bottom of the stroke. They worry that they don't want to put it too low.
If you look at pro rider's fits it looks like their saddles are incredibly low compared to most recreational road riders. Think about an efficient pedal stroke with your heel DOWN at the bottom, and you want more than just a slight bend at the bottom. Rules of thumb I throw out here, because it's where it feels good. Like I said, though, have some bend, don't worry about bend, you really don't want to be close to straightening your leg out. You'll know it's too low if you start experiencing knee pain after a few miles. Too high exhibits hamstring pain and tightening fairly quickly.
Those two concepts will go a long way towards the third, which isn't so much a fit issue as it is a posture thing. I meet so many riders who sit their butt on their seat like it's a chair. Do this and you'll find modern bikes difficult to fit for anyone except the exceptionally long-armed. What you need to focus on is a straight back...I mean, board straight. Then bend at your middle, allowing your pelvis to rotate forward, until you reach the bars. I almost guarantee you that you will realize you have 2 more inches of reach than you thought you did. See here:
http://www2.trainingbible.com/joesbl...e-posture.html
The kicker is that this posture is not natural for most people. It will feel good immediately, but after a few miles (or less) down the road you might start finding your body slouching. It will also effect how your saddle is tilted, which will require some conscience and work. You might soon realize that your core is not as strong as you thought it was. You might find that riding slight hills and really pushing the tempo makes it feel better and makes proper posture more easily attainable.
Over time you will develop muscles to hold the proper posture, and you will develop flexibility. It took me months upon months, but now I, a guy with short arms and supernaturally tight muscles, can't get my top tube long enough!!!
The last thing you should consider is a longer/shorter stem. If you apply all of the above, and spend a few hundred miles breaking in the concepts correctly, and then find you are still reaching too far THEN and only THEN do I think you should look to that recourse.
Fit does not come easily. Working with a bike fitter will make it happen faster, as they know exactly what to look for, but it costs upwards of $150. It's well worth it if you have it.
I think the most revolutionary aspect of posture for me was realizing my seat needed to be lower. When I lowered it my reach increased because I could rotate my pelvis without bad things happening.
Give it a shot and let me know what you think.