WarrenTrucks,
as you might have already read in some thread or another, Tim usually recommends either low or high output pickups for an SG, because they match the all mahogany body better than mid output pups (which might sound muddy). Insofar, you won't go wrong with either of the three Vintage pickups you mentioned in your initial post.
The RiffRaff places its strength in bite and crunch (in your words, they sound "sharp and trebly"), not warmth. If you don't like this tone, don't buy this pickup just because it looks a little "hotter" than the other two. When I was looking for a set of BKPs for my Epiphone SG, I found that in the majority of cases, Tim recommends going as low as possible. This means that he would recommend a Stormy Monday (even with "weak" Alnico II magnets) over a Mule (which is more suited for Les Pauls, I think). I remember one case where forum member "Fourth Feline" was looking for new pickups for his SG and Tim told him to put the SMs from his LP into the SG and to get new Pups for the LP instead.
I don't know what you mean by "I like to play with more gain...". The SM doesn't turn into mud when you drive your amp a bit harder (there are some very nice overdriven SM clips out there, indeed), so using more gain on the amp shouldn't be a problem. There isn't much difference between the output of a SM and the output of a Mule (output specs refer to the bridge pickup only) anyway. However, the SM is known to be a very "dynamic pickup", so you may have to hit the strings a little harder to push your amp...