Do you have a Haynes Manual?? Very useful for some things and will explain about the 'diff caps' which are, in fact, outer bearing retainers. They also serve to retain the oil seal and the 'o' ring to stop oil leaking past the threads. Most importantly they are used to adjust the end float on the bearings that in turn allows the correct measurement between the crown wheel and pinion. It's highly unlikely that anybody would have replaced a diff bearing because they hardly ever wear out, and if one did only the correct replacement would fit. There is no need to remove these 'diff caps' unless you need to adjust the end float or need to cure an oil leak. I do hope that you remember how many turns it took to remove it. Failing that, clean it up and screw it back by hand until it goes fully home and then back it off one notch. This should be ok. You will probably need to replace the oil seal and sealing ring. Before going any further I suggest that you look into why that drive shaft is fouling the box by getting a pair of correct drive shafts for your model just to eliminate the other pair.
If you don't have a history of what has been touched on the car in the past, it is best to assume that the previous owners didn't know what they were doing.