I got into the BOS bunker in hidden valley, did their quests, they 'like' me, and got to the point where McNamara is being replaced as elder. Every NPC says 'oh just wait', and I've read that it's about two days until the change takes affect...

...Except it hasn't. I've done a bunch more quests, done stuff, came back multiple times but it's still McNamara sitting in the chair.

Bureaucracy or just bugged?

It does take quite a bit of time for him to be replaced, but it will happen! Just do some more quests. I finished maybe two or three quests and went back.

The problem is afterwards - for me, it wouldn't give me the option to join or support me. Please let me know if it allows you to.

Howd you get into the bunker? I found the body and have the password, but I never get a response and it doesnt have the option to say the password.

Lock picking, being on a quest that tells you to go there (Wildcards MQ, others?), or head there with Veronica.