I got a 54cm 2009 Fuji Roubaix Pro a couple weeks ago and have spent some time trying to dial this machine in. I've noticed a few problems that I can't seem to get rid of - first, after about 10 miles or so, my lower back starts to ache, like what happens when you do too many weighted back extensions at the gym. When I ride it feels like I'm keeping my back straight. I didn't have this problem on my 56cm 1990 Bianchi Premio, even though I felt like my back was hunched and rounded when I rode it. I can't really hunch my back on the Fuji because if I do I feel a little too stretched out at my arms.
I checked a couple of bike fit videos (the most useful being the Performance Bike one, here:
http://www.youtube.com/watch?v=FAl_5e7bIHk). I noticed a couple of things - first, that my knees aren't in line with the balls of my feet at the 3/9 o'clock positions on the crank - they are behind them, even though my saddle is pretty far forward, almost at the max lines on the rails.
This can probably be fixed by using a zero-setback seatpost, but there's the second problem: when I look down at the front hub in my typical riding position, my handlebars look quite far back (about an inch while riding on hoods). My stem isn't short, and a lengthier stem might cause problems with being stretched out too much.
So what does this mean, and what can I do? Am I too small for the bike? Too big? I'm about 5'10", but I have a long neck, a big head, and relatively short legs (approximate 32" inseam). I've considered getting a fitting but I have a small budget and would rather not spend the $100 or so.