You’re going into a lot of effort with this engine, kudos. The question was asked before, but I don’t think you answered it. 1995 was the last year for the 28-oil-cooled alternator. Many owners did the upgrade to the air-cooled 40-amp unit.
I’m not sure if you know this, but the failure rate of the 28-amp alternator is high. If the upgrade is needed on your bike, the options for the parts needed to do the upgrade are harder and harder to acquire. The upgrade is not cheap and involves removing the swing arm, fuel tank, and numerous other parts to do the change.
1990-1995 model years had an external VR/R. It has a 6-wire white plug attached to it and is mounted on the frame near the battery box. If that is still functional on your bike, you need to make a decision on how much more time and funds you are willing to put into this project.
Tell-tale signs of imminent failure are oil seeping from the seal where 5 wires (3 yellow, a black, and a white wire) come out of the alternator. You can also test each phase of the alternator with a meter and compare your results with the shop manual. The condition of the white connector to the VR/R will also indicate whether you have a charging issue or not.
If the upgrade has already been done, great! You’re on the road to eventually getting one of the finest sport touring bikes made.