We all have advice, John, but to answer your question....it takes time, mistakes, experimenting, etc. to come up with the "right" bike fit. And sometimes, as your fitness level changes, or other physical changes occur with time and circumstance....your "ideal" fit requires further tweaking. It's always surprizing how sometimes what seems like a small adjustment can lead to significant results. Its good to read up on all the fitting information, but, in the end, it's you trying things and seeing the results that most counts.
Consider all the dimensions of bike fit: Bar height and distance from your saddle, width and drop of bars, where you place your brake hoods, saddle height, angle, and fore/aft adjustment. Also the width and length and curve of your saddle. Your cleat placement if you have other than just plain platforms. Some of these are more significant than others. So do some reading at Sheldon Brown, Peter White, Rivendell, etc. Don't necessarily be caught up in the "racing" bike fit. And don't think it is some erudite process that you have to go to Italy for and visit some bent over little guy who looks like Gepetto. Or the Trek windtunnel either.
It is not uncommon for bikie types to have a box full of stems, bars, saddles, seatposts, etc. they've tried and discarded. Some bike shops can provide you with valuable help, others not so much.
For sure, your body may just be responding to the new stress of cycling.