Thanks guys for your replies. This basically confirms my hunch about how the pedal combinations might play out: that I am better off with some kind of clean boost into the front of the amp than anything that would colour the sound too much. A lot of the distortion pedals just seem to sound terrible through my amp. Apparently I have one of the best ones, an EHX Metal Muff with Top Boost, but that sounds awful. A friend of mine tried it through his bass and loved it, but he basically expects to get it from me for practically nothing. I'm trying to get him to swap something or do some kind of maintenance work (I have an old Peavey Bandit with a bad solder joint and/or stuffed volume pot that needs work, and he's a wiz with that stuff) in exchange for the pedal. The best I would be able to get for it locally on the second-hand market is $50, and it would cost me three times that to replace it new. The irony is though that the Bandit is the only amp I have that it might sound good through!
I remembered you getting a HM-2 Dr. Pain and was wondering how that worked out. I think I will just go with an MXR EQ as a boost, given that I have two. I'm actually using my 10-band MXR (which I believe is the same as the Kerry King model except it lacks the stereo output) in the effects loop as a tone shaper before the chorus and delay pedals. I have a 6-band MXR that I received DOA from an ebay seller but basically ended up paying nothing for, but which I need to solder a new DPDT switch into. I bought it as a booster for leads and from what you say about the 6-band it sounds like it will be pretty good last in line on the front end of the amp. While it has less frequencies and no overall volume and gain sliders like the 10-band it does have 18db of cut or boost rather than the 12db on the 10 band, so I figure it will work well in that spot as a lead boost. I already have a screamer after the other front end pedals and that colours the sound a bit, but in a subtle way that I like and takes out some of the low-end boominess of my amp.
While something like the MXR CAE boost/linedriver pedal can also be used as a boost I think I am better off using that as an always-on buffer at the front of the signal chain. I'm wondering whether it should go before the tuner and the ISP or after the ISP? I guess that depends on how much noise it introduces into the signal chain. I have experimented with the ISP before the Polytune and found that it made the Polytune more 'flakey' and harder to get a consistent reading from (although this might be my imagination? Most tuning problems on an SG come from the G-string sticking at the nut and/or neck flex as you change tensions on other strings). I can run the MXR CAE pedal at 18V which apparently makes it even more effective. I basically want it before the phaser so as to provide a strong signal into that, as I hear the EVH model (and maybe Phase 90s generally?) can be a bit odd if they don't receive a strong enough signal.
Anyway thanks guys for your thoughts and when I have the 6-band EQ fixed I'll let you know how it worked out.