1. If you are running a R200 type diff, then any R200 diff (GT-R / GTSt / Stagea) should fit.
2. If you fit a 4.1 or 4.3 ratio, you will get better acceleration. In general, you would lose top speed, but it is possible you may get better top speed because the engine can more easily turn the rear axles through the lower ratio. But you will be revving the engine higher, regardless.
3. I would think that a 3.9 should be more than adequate for a RB20 in a car designed for a CA18 / SR20
If you are happy with the performance now, I'd say leave it be.