How much impact the pups have depends on how different they are. I've never gigged so I'm not an expert on this, however I'm not sure it's something you need to worry about, you'll very quickly get to know the difference in levels if there is any decernable difference and you'll know how much to tweak the volume to compensate, it's not really a phaf to move the volume or gain one notch up or down is it, it will take longer to swap you guitar lead.
As for taking the amp into consideration when choosing a pup, again probably not a big problem, it will have an impact on tone, of course it will, just about everything does, but frankly you really don't know what a pup is going to sound like in any given guitar either, you can only guess, same with the amp.
I really wouldn't get too hung up on all the variables, you'll drive yourself mad, have a rough idea of how 'hot' you'd like it to be, decide what tonal characteristics you are after and that should narrow down your choices. Always email Tim for an opinion, post a 'I'm after this kinda sound' thread, and see what people say. Don't get too put out if you don't get many responses, poeple on here tend to only post if they have something useful to say, if they don't know they don't make stuff up.
Going back to your original post about what guitars suit a hot pup, I don't think it works that way, the hotter the pup the more it will stamp it's tone on the overall sound, but you pick the guitar for it's qualities and then match the pup to complement them and acheive a tone. Feel free to bounce a few ideas around the forum, like ' I'm thinking about an SG with Cold Sweats', or 'I want to play super heavy Death Metal, what do you guys use?'
Use the forum search too, chances are someone has covered off at least some of what you want to know.
