Hey Miranda,
I definitely hear you about how one thing being off affects so many other things. It's a very personal example of the Domino Effect!
Can you videotape yourself while riding a trainer and take a look? Or maybe just pay close attention to how you sit when you're on the saddle. See if you sit squarely on the saddle, or if you're off to the side. Watch how close each knee is to the top tube when you pedal. See if the knees stay straight as you pedal. All these things can tip you off to funky posture, which may explain why you're sore.
Check with the Mayberry Man about the fitting! Where's the closest Bright Lights, Big City? Maybe there's a fitter out there that comes with the Seal of Approval from another TEer? Could be an excuse for a road trip!! 
Good luck on getting this straightened out. (Yes, the corny pun was kinda intended.)
- Melissa
I'll get back on the bike soon, I promise!