Time for another update.
I re-rerouted (third time's the charm...) that front brake line per 5twins advice and I must say it's MUCH better, thanks!
Got my chain, mufflers and air box rubbers, so I installed all those goodies and put the carbs back on.
I looked at the muffler situation and wound up installing them without adapters. I took the reducer that came with them off, and they tapped over the boss that's welded to the inner pipe where the outer pipe ends very nicely. Just a little gentle persuasion with a dead blow hammer. From there I was able to use the stock rear mounts with the hangar strap that came with the mufflers.
All the mounting stuff is tucked neatly away and I think it looks pretty good, other than that bit of ugliness right at the end of the outer pipe on the header. That's where the bottom drain holes are, probably a bit of scrubbing and buffing will take care of the worst of it.
When I cut the old mufflers off, I cut a bit further forward than I would have if I'd known exactly what was where inside the outer pipe. I won't know if that's gonna be a problem, rattling-wise, until I get it running. If it is, a bit of time with the welder will fix that.
So, a bit of clean-up on the wiring and it will be time to start tweaking and tuning.