it all really depends. I have an original 65 Mustang, and one that I built myself with Japanese pups. The difference between the pups *is* noticeable, but I'll play either one and still be happy. As for the trem, it's great for those little *warbles*, but teh suck for dive bombs. The tremolo is really meant for slight play/use. Also, and I mean this sincerely, *any* guitar can be a great player if you have it set up properly. I'm a huge fan of graphite and bone nuts, and I believe your guitar is only as good as the nut.
As for the '65 RI's, I'd have to say that the craftsmanship is better, as they have the old skool shielding in all three cavities and wiring is cloth. (Yea, I know...but, I really prefer cloth wiring.) I'm not too sure about the pups, though.
Anyway, as for mods, just get a proper nut...and play it for awhile. Besides, it *is* just a backup guitar, right?