All the time Vail spent on trying to make a Link between Rushmen and John Mahoney's character was just a waste of time?
I mean it's not like Arron/Roy killed Rushmen for anyone else except himself. He was a mad man who killed a perverted Archbishop. It was a crime of passion not profit.
Not all investigations end up being used in court. What you seem to have missed is the simple fact that he looked into a possible link between Shaughnessy and Rushman at the time he still thought Aaron was innocent. When he discovered that Aaron did in fact killed Rushman. All he did was outing their shady business by putting Shaughnessy on the stand in order to make him pay for having Joey Pinero killed.
As for the real motive is a plot hole to me. Because Roy was clearly not the kind of character that would take abuse from Rushman. So he clearly did not killed him for the forced video and he did not killed him either for the abused done to his fellow residents (since he killed Linda too).
So that pretty much doesn't make sense. The most likely theory is that he's simply some kind of twisted psychopath he either enjoyed making the video or didn't care and just killed Linda and the Archbishop for the sake of killing.
It's a big plot hole but it's pretty much an unavoidable.
you need to consider the "hearsay" re the boy who was abused by bishop 10 years before [the boy that Marty arranges to be in court so as to see Shaunessy go ape]
so bishop would not stop at one boy so Roy was most likely also a victim back then.
also this was the "bad bad thing" Marty did ie get the bishop OFF back then