looking nice so far, definitely plumb and wire the upstairs while you have easy access, won't cost very much and it can all sit for a very long time if you want.
The clearance issue would have only been mildly annoying. Easily rectified by adding an additional top plate run to the walls. Particularly if your walls are 2x4s. Anothe r2x4 flat on top, or even an 4x4 or 4x6 etc if necessary. Annoying and not what you paid for, but easily and quickly corrected in a very short time, especially if you were paying for crane / boom time to get the trusses up.