I'd go w/replacement/reproduction of the damaged or missing parts; their presence (or absence) degrades the rest of the set and detracts from the work and talent you've expensed in the restoration thus far. Regarding your situation, consider you've got an unstable foundation right now and as such, it may put added stress on other mating surfaces and joints. If repairs are undertaken further in the future, they may be doubly difficult as a result of the minute distortions that occur. I agree with the assessment on stuffing caps; besides, unless you're going to have the underside of the chassis on display, why bother? I've compromised on a few of my older sets: I saved the pulls in a Baggie labeled with the set and restoration date. No mess, no guilt. If you've got room, toss 'em in the back of the set for safekeeping.

Good luck!

Michael