Jeff, FWIW, with transom complete I found zero interference of any kind, tend to agree with Arban, installing final frames, door, etc., helps greatly establishing final sweep of the hull, establishing spacing for rear windows and even finishing up internal deck beams as well as the Y8 instillation that Arban mentions allowing everything to be tied together.
Also, I found you cannot completely trust the jig supports as to spacing before you glue[pin] them. Here I pulled the transom sheet with window cutouts to get my spacing fairly accurate with modest tapers top to bottom on outside timbers.
Course, big reason I went that course was to do outside planking to give hull greater strength but all went reasonably well.
Jumping around somewhat avoids tedium as well.
Keep her going.
Tim