The Warren Haynes mod is a simple switch for the 1nF bright cap on the gain control. It's not a bass boost, as Bonomassa thinks. It's just a bright switch. But I suppose flipping the switch might give the illusion of more lows by way of cutting highs. Even Warren Haynes had no clue what it was. He stated:
"My modification gives it a lot more low mid-range at a low preamp volume... I called Mike Soldano and said, 'I'm having trouble getting enough bottom-end, otherwise I love the sound.' And he said, 'Well, that's really strange, where's your preamp set?' And I said 'It's set on two and a half or three.' And he said, 'Oh, well most people set it much higher.' I see but I don't want that extra dirt. So he said 'Great I'll make a mod to it. So he made this modification here. I had him put a switch where you can flip the switch and it's a stock Soldano or you can have my modification. But all my Soldanos have this mod and it just gets much more beef and a little preamp gain. When you do this, you can set it way cleaner and have that girth. I don't like the really overdriven sound."
But it's just a bright switch.
Bonamassa is also running that amp with a step-up transformer to get 220v. But the amp is wired for 240v, which means the B+ is probably 40v lower than where it should be.