Well Sir,
I'm assuming you're trying to do the final assembly when the steps are full extended, correct? It would be pretty hard to do it when they're retracted. Now, I don't know if they're all equipped with them or not but, at the sides of most Kwikee steps, (at least the two-step models)there is a concentric adjustment. That adjustment is what limits the step travel, along with the full travel of the motor, in the extension mode.
But, if those concentrics are holding your steps from aligning all the parts, you may be able to back off on each side and maybe align things easier. Just a guess.
Scott