I'd shoot off an email to Mesa Boogie support while waiting for responses here. They did bother to forward one of my earlier requests to the technicians, and I got a good answer from them. They might be able to confirm that your output is too weak.
Since you seem very competent with tube amps and you have a scope, you could try to check the OT by using a signal generator and your scope to analyze the turns/impedance ratios? I think this is possible without even disconnecting anything, right? Although since the primary winding is connected to the plus-side of an electrolytic cap in the power-supply, you would have to make sure you did it in a way that doesn't put any negative voltage on the cap, since that might damage it.
Hope you get it sorted out soon! You mentioned playing it a lot, so its not so cool if this takes long.
PS: Stay tuned! I just checked the manual for my multimeter, and it says that the AC setting is good for up to 400Hz. So I'll try to generate 400Hz from my computer soundcard and see if I can get a reading on the output of the amp. I have a powerful L-pad to use as a dummy load, and it allows me to hear a little bit of the signal. That way I can hear if it is clipping or not. I'll definitely do it in 5W mode. Possibly also in 25W mode if I trust my dummy load, but a 5W mode reading should be enough to confirm that your amp is damaged (if it is). I'll be able to do it this evening. I'm in Norway and the local time is 20:00 now.
EDIT: Just did it in 5W mode with a 400Hz signal. I wasn't able to surpass 3.8V on my multimeter at 400Hz. If that was a true RMS reading, I guess that corresponded to P = Vrms^2/R = (3.8*3.8)/8 W = 1.8W. At that level I could hear quite a bit of clipping.
Maybe nothing is wrong with the amp? Although I would be interested in hearing from Mesa how they got 5W out of it... Btw, the power tubes in mine are not stock, they are JJ's.
Maybe "Mesa Boogie 2:15" doesn't sound as good
Torquil