I never did figure out what the misalignment issue was while taking the cab off. My "helper" during that phase was my wife, and I was pushing my luck getting her to agree to be my extra hands lifting the cab off off the frame with an engine hoist.
I've gotten the cab back from the chemical dippers, and ordered patch panels this morning. Looking at the bottom of the cab, I don't see anything obviously bent... the body mounts are all straight, etc. Time to measure the frame I guess and compare to the FAM dimensions.
Any recommendations for the following problem areas? Thankfully my floor is very solid, only a bit of pitting on the surface. Rockers are "mostly fine"... I ordered new ones, but tempted to try and just fix the pinholes rather than cut out the entire rocker and risk changing the overall alignment of the door openings. I believe I'm going to try to do the inner/outer cab corners first as that seems like the easiest for a beginner to tackle. My intent is to butt joint everything and use as little filler as possible. I don't want this to be layer upon layer of bondo like what got stripped OFF it.