G'day! I haven't ever really been happy with my SD-1 into my Marshall. I modded, and modded.and modded it, and finally did this one (not exactly what you are looking for I know, but it's the best I could come up with).
I can recommand MA BOSS SD-1 regular mod - it really sounds great to me. Also you can easly transform SD-1 to TS-9 or TS-808 - but I am opposite to moding Boss to Ibanez - Boss SD-1 has its own sound so why transforming it to Ibanez? Moded SD-1 sounds great, I have TS-5 which is identical to TS-9 and can say that moded SD-1 eats both. But!..moded BD-2 eats moded SD-1 but costs much more So if you are looking for "top end" overdrive get BD-2 mod it and you will have heaven in your ears
what are the current clipping diodes failing to do? i think they do fairly well with most marshalls. attempting to switch out the diodes without reducing/increasing gain is going to be a challenge.
ah. the 6100's are one of my favorite marshalls of all time.
the gain structure on those should work with every pedal from the boss line with the exceptions of the DS-1 with the tone knob set too high and probably the HM-3 (both of those use 1N4148's I believe).
i'm not really certain what you mean by warm tube clip, as the SD-1's 1N4148's are pretty warm imo. the two options you are probably looking at would be 1N34A germanium diodes (reduces gain and less "boost" feel) or 1N4001 rectifier diodes (increases tube crunch feel, but also increases gain and bite). the fulltone fulldrive 2 uses 1N34A's in series with 1N4001's to help smooth off the bite of the 4001's. 1N4001's are the usual component in marshall/mesa type pedal mods.
you could always convert over to symmetrical clipping...