I can't think anything about why did it happen...I meet this type of driveshaft on many R4s and I have never had any problem. The smaller diameter inner CV joint is typical on GKN/Glaenzer Spicer driveshafts.
As for the differential caps, they are not screwed too tightly, but have an O-ring on their inner circumference that causes some friction. If you can't move them by tapping around with a blunt screwdriver and a hammer, measure the inner diameter of their spline, drill at that distance two holes on a steel square bar of sufficient length, then screw two bolts in them. Now you have a nice pin spanner...for better fit, file the bolt edges square so that they fit the spline teeth exactly. This and a little WD-40 should loosen the caps.