Not quite thread necromancy, but close - sorry about this! Just noticed these questions several pages down the thread, without previous direct answers.
1) Vulcan is a member of the Federation. There were no extradition procedures? They couldn't just insist the crew come back to face charges?
I'm sure they would - which is why the crew would balk, and exploit the already established Vulcan hostility towards Starfleet and the ability to pull a string or two ("Amok Time").
The charges would be pretty serious, and would certainly end the Starfleet careers of everybody involved. The decision to face the charges seemed to have been arrived at by voting. It may have taken a lot of time to reach a unanimous vote - Kirk still feels the need to check when the heroes finally launch. Given the fact that our heroes had demonstrated their loyalty to Kirk over loyalty to Starfleet, they may have seriously considered allowing their careers to end without the formal trial, and proceeding with a different lifestyle where they would remain associated with Kirk and perhaps make use of their prize vessel.
However, I would argue that the stalling was chiefly due to the slow healing process of Spock. The mutiny had been all about rescuing the half-Vulcan, and would not come to conclusion until Spock was back.
Or send someone to get them? McCoy says they "could have at least sent a ship" but why didn't they?
This probably refers to the final few moments: Kirk and pals decide to surrender, tell Earth they're coming, and Earth fails to respond. They shrug and decide Starfleet must be sulking, then board their own vessel.
2) Saavik was not implicated in any wrongdoing. She was the sole survivor of the Grissom. Surely she would need to be debriefed ASAP. Would Starfleet just let her hang around for 3 plus months?
We don't know that she would have been hanging around for any length of time. If she only recently arrived (perhaps with news that encouraged Kirk to return), this would also explain the next point:
3) It took Saavik 3 months to say some vague words to Kirk about David? 3 months to finally get around to telling Kirk what he already knew?
Moving on:
4) I understand the necessity of presenting an operational BoP to Starfleet, but why do all this work to drive home from Vulcan?
Because Starfleet didn't send a ship, and taking one of their own would be just as easy as taking a flight on a Vulcan ship - and possibly quicker, if there weren't frequent regular flights?
Why completely reconfigure the bridge for such a short trip?
Here I'd argue it's just a different part of the ship - the wheelhouse instead of the intelligence operations center.
And what happened that the BoP needed 3 months of repairs?
Probably Scotty happened. It's not that it took 3 months to repair the ship - it was that Scotty had 3 months to spend, and spent them repairing the ship.
5) After 3 months, Chekov is the only person to change clothes? Maybe it's not the Klingon stench McCoy needs to cloak…
Those clothes might have been fundamentally unsuited to the Vulcan climate, and thus never worn during the exile. On the other hand, the local clothes would not be Kirk's first choice for wear when returning to face the charges.
Spock could still be seen as just as recovered in a week as 3 months (those damned Vulcans shake these thing off so quickly).
But making it three months does add to the impact...
Timo Saloniemi