have you checked the pre-amp tubes as I suggested? try changing them with one you know is good?

Try disengaging the PAB, turn off the "deep" and "bright" switch. Keep the "Volume" and "Overdrive" know below 5, lower the volume on your guitar (what pickups are you using?).

What speaker are you using?

M.

Damn, I would never guessed that's an OD pedal. What is it?
It sounds very Dumblish to me. 

If you don't want to mod the amp it self, like Marin said, tubes, speaker and pickups are the things you can tweak.
 

Not exactly... OD tube would affect only the overdrive sound

Tough question... you have Tung-Sol in there, right? That is suppose to be quite good tube.

Maybe this will help...
http://thetubestore.com/12ax7review.html

 

I haven´t been following this topic very much (and I´m too lazy to go back a few pages), but have you tried checking and adjusting the OD internal trimmer?

I don't have mine yet, but this is a comment from an OTS owber:

 There are three internal trimmers inside the chassis. Two blue and one black with a whiter center. If you are looking into the chassis from the front of the amp, the BLUE trimmer on the far left (on a small board actually mounted on the left side of the chassis) is for the FET channel and Nik states that should be left "high" which is at least at 12:00 and that is how mine came set from the factory. (I haven't experimented with the FET input yet by the way) Moving to the right from the first BLUE trimmer, you'll discover another BLUE trimmer that is on the MAIN circuit board and is located just below and slightly to the left of the second pre amp tube socket (V2). This is the OD trimmer. It is very easy to adjust, (small slotted screwdriver will do) and mine came set (stock) from Nik at 9:00. (basically the slot was straight across) The OD trimmer has a HUGE impact on the tone, volume, and overall vibe of the OD channel. Set too low, (I found 9:00 o'clock too low for my ears/tastes) the OD channel sounds thin and anemic, (even with humbuckers), at volume levels that will get you invited back to many a gig, but the OD channel does seem to come to life a bit at that setting if in fact you do CRANK up the amp, but holy crap is it loud when you do that. Set too high, and the OD channel comes ROARING to life at pretty much any volume, but it VERY QUICKLY moves away from Dumblesque heaven and into Marshall mayhem in a big hurry. Don't get me wrong, the amp sounds great a pretty much any OD trimmer setting (VERY versatile) but it does take some time to dial in the OD channel using the OD trimmer, level, ratio, volume and master volume as well as tone contols set to taste obviously.

new clip. These are tones I like: