The VTM is a good amp. The other guitarist in my band uses a VTM120. It's like a cool-biased master volume JCM800 2203/2204 with dipswitches for the most common mods done to 800's. (I still give him shyte for playing a Peavey though.

)
If you plan to use much fuzz/OD/dist, I would suggest pups with DC readings below 14K or so...above that they are tricky to get the fuzz right. If you're doing the guitar straight in, just find the pup which works best for your amp and axe.
That said, an SG or LP style axe with a Custom at the bridge does a good stoner sound. The low end stays together as you tune down to D or even C. As you go to C or below, I'd look toward a 25.5" scale axe to keep the string flappage to a minimum (unless you really want to sound like Sleep's Jerusalem/Dopesmoker....

) Though Wino used an LP Custom for most or all of Spirit Caravan and The Obsessed, and he sounds pretty good IMO.