I have had my SD Hotrail in my strat bridge position for a long time, but i've always noticed that it doesn't give me as big a sound as others who use it, it sounds more thin and trebley (sp?). Do you think it could be out of phase? if so is there a way to change that without taking off the pickguard and everything?
No, you have to take it off. Come on, its better than having to take something out the back...
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but others who use it probably don't use a Marshall MG

I have a SD Hot Rails in my strat too and it sounds great trough a Roland Cube 30 / Line 6 Toneport UX2
I just installed one in my strat yesterday, I haven't gotten to test it yet, but the schematic says to reverse the green and black wires it's out of phase. So you would have to remove the pickguard, but if their not old, and your careful, it is possible to re-use the the strings if you dont have any, just unwind them carefully and don't take them off the bridge since you'll never get them through there again due to the curly ends.