Im going to try and help you the best I can, being a lefty strat player, and a hobbyist, I'm going to do my best.
First off, your tremolo is a standard left handed one. I think your talking about the wammy bar itself.
whats the double sided tape or whatever on the headstock?
and when you say you cut a hole in the bridge do you mean the pickguard?
as far as comfort goes, you wont have the usual arm rest on the side, it will be more like a Telecaster. But with the bridge a bit further away. a Similar feel to the LP you have(Nice BTW lets see more pics)
why HSH? ever look into the compact stuff by SD? My strat uses the duckbucker humbucker and a set of high gain hotrails.. Killer..
anyway
Questions
Q.1
Your Tremolo can use the same 6 mounting points as the vintage trem you have, but the offset for the bar will have to be widened( notice the trem pocket is slightly wider to accompany the bar, but the sadles are still centered with the mounting screws.) a simple router will do this, but you will see the gap on the other side. Personally, the reason SRV did the same swap was because he and Jimi wanted the bar to fall over the bridge(well, Jimi HAD to have it like that). So id just leave it.. It looks more Jimi anyway.
Q.2
Understandable, whenever I play upside down strats I notice the cord rubbing my arm and annoying me.
to do what your saying you'll need a long drill bit to get to one of the cavitys(the existing jack cavity being the closest) and it would be a impressive mod to say the least.
Q.3 Volume and tone controls:
I dont see why the bar would get in the way, unless you mean simpy using a lefty bar on the right handed trem, it would be in the way as much as it is on yours.. but thats only if you tighten it and not let it sit flat.
when you said tremolo earlyer, did you just mean the bar?
as far as a kill switch, a simple push pull pot can be wired for that.
Q.4
asuming your repainting the body(witch with routing for the trem pocket, if thats indead what you ment, would almost be required) otherwise, I think Id just leave it.. nothing else would look right..
Q.5
a hammer.. seriously..
its possible its glued on and there are a few things, like heat or whatever, but im not versed enough in that, mine came off with a good wack to a flat head.
Q.6
a router, obviously
witch way is the bow? for mine I turned it clockwise when the action was to high..
why do you need new knobs?
and dont forget your going to need to drill a new spot for the strap button.. otherwise it will flip over on you while playing(at least that what they do for me!)