I keep getting that he respects me, glad that I've taken up his ideals, and that he wouldn't want to go into battle with anyone else, etc, etc. But I don't yet have his perk showing. Is his perk known for being bugged?

You also need to complete the Brotherhood quest Blind Betrayal before you can max him out and get the perk. Have you done that?

No, not yet. Can you do that one/go that far without being kicked from the RR or Institute? Am planning on trying for the friendly ending between the RR, BoS and MM.

As I recall it's before the point of no return for the BOS with regards to the Railroad. As long as you don't report to Captain Kells, you should be fine. Save fore handing in Blind Betrayal just in case.

Thanks

I wish you could have gotten that perk before that quest.