"Can the taillights on a '94 be swapped for the newer round style or is there a massive hole in the rear body..."
You could probably just fab up a backing plate to cover any holes left, but it's my opinion that the older style are better units anyway.
The newer style are notorious for filling with water and crud and shorting the bulbs out. It's even possible for the short to be so bad that the ECU can be damaged.
Here's more on that:
There is an upgraded socket available with a bit more protection but I think you should still drill the weep holes just in case.
Also, if... there's diamond plating on the front fenders, can they be removed and holes patched?...
It'd most likely be easier and cheaper to just replace the entire fenders. The wingtop protectors are installed by drilling into the body. Again, in my opinion I believe it's better to leave them on. The aluminum wingtops are very thin and susceptible to dents with very little pressure as compared to the steel fenders of most vehicles. If you own your D90 long enough you'll probably end up with tiny dents in the wingtops anyway. Even if you're very careful, there are times when others may be accessing your engine bay and unknowingly leave a dent by leaning on the wing tops. With the protectors in place you can stand on the wings.