I have IIc manuals but need to check which language they're in. However, these manuals never say much about alignment.
I have used these Focomats since the late seventies, still do and I know many photographers who use them too. Something really bad must have happened if anything went out of alignment. Generally all is ok: the automatic focus, the lens stage and the bulb. Set up is quite easy, but it depends a bit on how much you need to put together. I guess you should just try, there is nothing you can do wrong except for sliding the lens stage from right to left: you MUST lift it upwards and ONLY THEN move it to the left. Look at the small arrows! Unfortunately it is possible to simply move the lens stage sideways, but when pushing it towards the left it releases the Bowden cable which causes a round metal part to jump out. This part should land ON the cam, but if one did not lift the lens stage upwards it lands AGAINST the cam. This causes heavy strain on the cable which results in the cable breaking much sooner than necessary.