Thanks for the reply, I actually encountered (and got past) both of those issues you mentioned while working on the bike! I initially installed the cages backwards; worked it out almost as soon as the BB was reassembled. Then when I put the old bearings back in, one of the new cages left a ball behind in the race, which was removed when I found out.
What would you think about removing the cages altogether, as they seem to be causing more problems than they solve? I didn't know you could do that until I did some further reading here.