Are the seams of the 'squat "U"s' middle top and center, or fore and aft ends? btw I'd use Dow Corning 795 for that step rather than butyl.
Assuming I'm picturing this correctly:
I would mark the edges of the frames on the port lens, and mask both sides of the new lens to that line (or cut the protective paper to that line) leaving only the edges exposed. If the gaps in the frame are fore and aft the 'sliding displacement' should be minimal. Now mask the outer edges of the frames (ie "U"s) and generously goop the grooves . Then slide all the pieces together, and use a soapy gloved finger (
) to tool the sealant all the way around the joints, wiping up the excess.
I'm assuming that you'll need to 'seal' this assembly into the sandwiching frame halves too... use a similar technique. Spending an hour or more masking will pay off in cleanup time and resulting appearance. Butyl may work there too, though.
Of course, could be I'm completely off base.....