So at the very least, if Beastie could adapt those to be in the ToD/SoM palette style that would be fantastic.
Sticking to the D&D arcade game styles will be best. Maybe I can do it using a method like Don Vecta said. What we could do thou, is get the master palette for the original D&D games from MUGEN, and just choose colours from that for the remaps.
Some chars will be harder than others thou. Matching them to the D&D palette and style is also trickier and heaps more time consuming than just making custom pals OTOH.
just rough test edit based on the other sprites pal.
D&D: TOD Based Palette
(skin colour and reds from the other players, dwarf etc.)
other tests
(they probably have too much colour now compared to D&D sprites)
custom style
You guys already have lighting effects, so if you add minor/varying darkness overlays to every stage this actually helps sprites blend in with the background too, even on the original D&D stages.
About getting palettes from mugen...
for example this is TOD pal.

If you can also get/make a master palette for all the IGS sprites, you could convert all of them to use this master palette. Then edit each colour one by one and swap it for colours in the D&D master pal. Just swap IGS green for d&d/capcom green etc. etc. Then all you have do is remap them all to this pal, or convert them with PalApply.
When trying to do a mod like this one of the problems is not having enough sprites so you have to do a combination of ripping, making your own, and using sprites from other companies to tell the story you need to tell. For example, if you need a medieval town background, and you can't draw your own, then you're stuck using what is available, whatever the source.
It's a fun way to make a game, but it can be very hard and frustrating too I know, I've attempted a few mods trying to mix sprites too. I usually end up with a lack of sprites that fit. That's why I was just trying to show some easy methods I use to help things fit together. I'm suremy methods probably aren't the best, I'm no expert with colour, I usually just do whatever looks good to me and try to keep them roughly the same format.