Oh man, those stupid overly-complicated linkages can be a pain. I chased mine all over the place for years and finally figured out by accident that someone previously had put the linkage that goes around the sway bar on backwards. Now, one of these days, I'm going to have to go over the whole thing again and hopefully get it working right finally.

Lots of things can affect them, and you may find that setting everything to the "FSM measurements" doesn't work either because of wear throwing it off.

You just have to take each piece one at a time. And yes, definitely check seemingly unrelated things like the engine mounts. There's also the firewall pivot to look at, and the pedal itself, which can get wonky.