toyota nova

Howdy folks, I recently changed the head gasket on a 1988 chevy nova, and when I got it all put back and timed, the automatic trans doesn't seem to shift out right. I marked all of my vacuum lines, but quite a few lines lost their markings. I have been told by others that this is the problem, all the books or schematics that I have found are very vague on this subject. If anyone out there knows anything about this type of car or subject, I would really appreciate the knowledge. The motor is a toyota 1.6 4alc.