I have good news and bad news. I ordered a custom F-50 last year (wood & wicker) and after the first couple of months this started happening for me too. I did the whole tube diagnosis thing, and ended up replacing the me all. The problem continued. Here's what would happen for me - about 2 hours into a gig or rehearsal after running the thing pretty hard it would start stuttering. Not a volume drop, but a complete shut off of sound. Lights all on etc, just no sound intermittently. Turning the amp off for a couple of minutes would bring everything back to life, but it would always happen again unless I shut down for over 30 minutes. Sounded like a hard tremolo, but not in a good way.
The first tech I took it to sat on it for 6 weeks and couldn't get the cutout to happen for him. I took it back, and first gig out, the problem reoccurred - not a good thing to have happen at a gig. Fortunately I had my DC-3 as a back up.
Took it to a different tech. They were able to get the problem to manifest. They were stumped as to the source of the problem, and ended up calling Boogie. Turns out there have been numerous problems with a batch of C-90 speakers. I'm not fully convinced that's my problem, but as I write this a new and supposedly upgraded C-90 is being installed in my amp. It's covered by the warranty. Sounds to me like you're having the exact same problem I was.
Before you take it in, do all the usual things like verify it's not the tubes (I actually did have 2 bad preamp tubes right off), make sure your cables are all good, and ideally just run it guitar>amp and take everything else out of the chain. If you still have the problem, I'm willing to bet you're having the same issues I am. (Boogie has said that ifit's not the speaker, the chassis is going to have to be shipped back to Mesa so that they can look at it - not something I want to deal with at all.)
I orded mine March last year and got it in June. Apparently serial numbers above and below mine have had these speaker problems. Good luck. I will write a detailed post to all the F-50 folks on here once I get mine back and have verified that the problem has been fixed.