I've dealt with some of this, myself. Funny thing...I got a new road bike in Dec. that didn't see the light of day until recently. On the trainer I actually thought the reach was a hair long...outdoors I discovered the opposite to be true and swapped my 80mm stem for a 100mm stem...SO much better! But my neck and shoulders are definitely a little achey. My leg muscles are hurting in different spots now, too, since I have to balance...and my back is definitely a bit stiff.

All last Summer and Fall I was very diligent with regular core work, as well, so part of my issues are almost certainly due to slacking on that for many months. When my core is strong it takes care of a wealth of aches and pains.

The worst thing about riding outdoors, though...the lack of fitness. 50 miles/week on the trainer can't touch 100-200 miles/week outdoors. I am sure a slowpoke now!