I think I would prefer to have the rubber drive shaft bumpers, under the premise they help to keep the splines centered. I haven't taken my pump off the hull yet, have done the oil and was glad the bolts came out without damaging the threads. LOL, you're supposed to use locktite blue on the threads before installing the bolts but I used anti-seize compound. I rarely ever experience lost bolts, unless maybe the threads let go in which case a helicoil would be the solution. Maybe I have special touch for knowing how much torque is enough, rarely strip threads unless they're already well worn.
So if you lost bolt(s), did you follow the factory spec torquing procedure, did you use a calibrated torque wrench (not a chepo harbor freight wrench, but something verifiable to a national standard and recently calibrated by an authorized shop to the standard), and did you use fresh locktite of the correct type as specified in the service manual? Did you use new fasteners, including new lockwashers (technically speaking, lockwashers are a one-use item)
I have to admit I do like reading and following factory procedures but as far as torquing and fastener selection goes I have my own established procedures and rarely have problems but I pay attention to the troubles others have so I know what to look for. For instance, the exhaust manifold assemblies seem to be tricky, to the point where it's important to use new fastener hardware and of course new gaskets. I don't want water in my engine if I can avoid it, so that's the one area where I would follow the factory procedure as closely as possible, because it's so critical.