I did work with the end caps separately, and it was hard enough to get it into cap 1 in the first place, then when I pushed the cable through the housing I realized it would be impossible to get it through the 2nd end cap since I would have to work from the inside.

I did not trim the cable though, that must be the missing piece of information. I don't have all that much leeway, the extra cable beyond the RD locknut was not too long, and now that I've frayed it worse I probably can't get a good trim. I'll give it a try though, now that I'm resigned to LBS doing it for me, I've got nothing to lose!