I think it is a matter of getting the signal path as similar to his, ie Fender twin, Mac clipping, pickups etc.... Then process it through a typical boss type OD circuit with the tone rolled off. I would think for you it would be to roll off your tone and mix in the distortion to taste. That is if you are going for his distortion style. I see Jerry having a pushed clean tone OD (before 1990's) with those pedals added in to top it off for a distortion tone.
From what I understand Brad designed this OD to add that mac style clipping which was Jerry's cleanish OD coming from unreasonable voltage levels in his gear. Getting that mac to clip right is adding harmonics to his tone, rather than using a pure clean tone. Something small bands just can't achieve musically due to the volume. I also remember him saying he made it versatile enough to dial in some heavy crunch like an MXR Dist+. Then from that base clean OD tone, you add in more OD signal, roll back the tone and there it is.
I guess the question is, which era are you talking about ie.. 1970 sizzle coming from a les paul into pushed twins, late 1970's to early 80's(mesa Boogie debate) mid 80's to early 90's or Jerry's 90's rack straight to the board. Are you talking about a distortion like I need a miracle or slipknot solo from one from the vault? Or maybe the distortion from the 1970 version of Casey Jones from closing of Winterland? all of those kinda different from era to era, imo.
I think the one thing that stayed the same for his "horn like" tone was his tone pot rolled back , plus a twin, a mac, Diamarzio humbuckers, an OD/distortion pedal and JBL's. I would like to see some pics or verified boss OD settings too. Oh, later on he was using an EQ in the path of the dist pedals. There was a thread recently about his GE-7 settings that may have some of those pics. I will edit post with the link in a minute,,,,http://www.rukind.com/forum/viewtopic.php?f=419&t=9679#wrap