So immediately Grady put some inserts in my shoes, moved my cleats around a bit, and raised my seat several CM.
It took about a week before the new stem showed up, but I got that put in and subsequently managed to do 55 miles in 2 days, with only minor back soreness while riding, and no lingering back soreness post-ride. Overall an amazing comfort difference! I know I'm still working on breaking in my sit bones, but he liked the stock saddle on my Allez Compact based on my size, and I bet that once I manage to get down a few lbs it will help me handle more seat time as well.
Overall I can't recommend getting a pro fit enough, I had a good time while there, and feel like I can put in more time on the bike.