I think that was where I went wrong, the engine wasn't bolted to the k-frame straight and it all went downhill from there. If I would've installed the k-frame and engine separately, that would've been more obvious.
Just like this TB thing - I started chasing an out of line k-frame when all I really needed to do was make sure all the bolts were loose and just tap it in.
I have the suspension, steering column, clutch linkage, all installed now and everything lined up fine.