rocdoc

Hi everyone,
I've been on an interesting journey of learning about the proper fit and the right way to ride a bike. So, after trying a couple of bikes, figuring out my correct measurements, learning what I'm happy with, I find myself about a centimeter and a half short (or long) of happiness (insert Anthony Weiner jokes here).
So, my ideal effective TT is somewhere in the 54.5-55 zone, and I have a fairly proportional body (height/inseam ~2.1, arm span ~ height), C-T ideal ~55 (I'm 5'10", inseam 33). I ride primarily on trails, some road and sidewalk commute time, not aiming to race. Went with a cyclocross bike to handle the uneven and some unpaved trails, and sidewalk bumps.
I bought a Fuji cyclocross bike (Cross 3.0) on a good deal at Performance. I had been between two sizes: the 54 has a TT (effective) of 54.5, C-T 54, stem 10. The 56 has both TT and CT at 56, stem 11.
I first tried the 54. I thought I felt a touch cramped, but that may have been just the new shape, I can't be sure. I also had an uncomfortable amount of toe overlap (size 11 sneakers - I use toe straps, not going to clip in any time soon, I do mostly touring where I like to get off and do some site seeing with my riding). I exchanged it for the 56. Initially it felt a bit better, but with long rides I feel that I am stretching a bit and "feel" it in my shoulders.
This has not been enough time to be very sure about either frame, but if I am considering an exchange I need to decide very soon - I do have a month, but I don't want to return a bike that's been used that long, they've been nice to me and I want to do the same.
Summary for the two sizes: Better with the 54: Tighter shoulder angle, making me feel better supported; narrower handlebars are exactly in line with my shoulders; Less reach to the handlebars, allowing my shoulders to relax a bit; more SO clearance. Better with the 56: better saddle height "feel" - I like it high and pedal with the heel up, and I don't want too much drop to the handlebars; less toe overlap and more stable, longer wheelbase; allows a straighter back, which is my preference (I am plenty flexible, I just like my back straighter for some reason).
So, is a shorter stem by 1 cm on the 56 going to take care of the difference between the two? Is this level of nitpicking over the sizes appropriate here and at my level? Or should I stop wasting time and ride instead? It really seems that I am 1 cm or so in either direction. Experienced riders might be able to extrapolate how much better or worse either fit can get long term - for me this is the first bike with road(-ish) geometry.
Thanks a bunch!

PS they did offer a "fitting", but it consisted of the bike shop guy eyeballing me on a trainer and going "yeah, looks all right"...