If you were to put the stock side covers back on over that reg would there be enough airflow? I want to put the covers back on my bike but I'm concerned about cooling. Also slightly unrelated. Is there enough airflow behind the stock covers to run my unifilters? They don't seem to touch the cover at all.
I don't know what regulator (or is it a regulator/rectifier combo) you have, but if it has a heat sink with cooling fins, it should be just fine.
A picture would be helpful, but as long as the filters have a reasonable size air flow path, they should also be good.