Bryan, I read your post twice and I still have no clue what you are saying and I fit bikes. Basically, when I read what you said I think you are saying the bike's too big (seat forward)...but when I read further, I get the opposite opinion. Longer stem. Why have the seat forward and then put on a longer stem?
Who fitted you to the bike? What process did the bike shop go through to determine your size? Why not move the seat back?
See a fitter...I do not mean to be offensive, but you need to see someone who can sort this out for you.

Have you been fitted, ever? Or do you know how to fit a bike? My guess is that, all these years you have been riding an ill fitting bike with a bad pedal stroke and have acclimated to it the best you can. About 10 minutes on a Cyclocomputer would graphically show you what your pedal stroke looks like and a good fitter would fix it or tell you that you bought the wrong size bike.

Last, you provide no sizes on either bike and if you bought a different size in the Madone (BTW...Trek measures their bikes differenlty than Bianchi), why?