I'm currently working on a production of Buddy: The Buddy Holly Story. Where we only have actor/musicians, and our MD sometimes plays pit piano (backstage, rather than a pit) and onstage for the final concert.
Some things that have come up. We have a few musicians who are not apart of equity, that were cast as actors (2 of the Crickets), one is part of the musicians union. Now, I'm not sure if any of you have worked with a Musicians Union, but they are very strict, which is fantastic for musicians. But, one of the rules is that only other members of the Union can play with them. We received a lot of concessions from them for having these musicians, especially since we're not using a pit at all. Now, they originally said that it was going to give them provisional status, but when one of the actors went to sign the forms, they forced him to become a full member. And wanted our lead (Buddy) to become a full member, but he refused, he would not join the union at all. Thankfully they only pushed for those two, but they technically could've got everyone (minus 3 actors) to join (only 1 if you count claves and guillero as instruments [we consider them props]).
Also, another issue has come up (not from the actors themselves, but a friend of the company who is involved with CAEA brought it up). Should Actor/Musicians get a premium for using a special skill like that (especially with the salary that musicians make). Also, should there be clauses that makes CAEA (or AEA) and whatever musicians union work together to create rules and standards for Actor/Musicians who are apart of Equity, but not the musicians union?
To answer the OP (even though it's been over a year). We have an Assistant Deck Sound guy and he is in charge of all the instruments, and he tunes them all up (the 6 guitars and 3 basses), the drummer, fiddlest, saxophone players and trumpet player tune their own instruments. The guitars all have the clip on tuners incase something happens, and we have a backup guitar incase one string breaks (because this model, is not able to be played if any string breaks at all).