First off welcome to BansheeHQ!
1: As far as head mods go, you can either buy a cool head and correct domes OR have your stock head milled. Me personally I run a Noss Cool Head and love it. Just really depends on how much your budget is.
2: If you don't see much water I prefer ditching the entire air box and running open k&n with outerweared pod filters for maximum air intake. If you do see the occasional puddle you could possibly suck water having it set up this way just fyi.
3: Boost Bottle= Trust me, the stock intake tube works just as good and boost bottles can possibly crack your intakes resulting in an air leak.
4: IMHO getting the TORS off the bike should be a priority. Look on top of your carbs, if there are big ugly boxes on top then you will need the removal kit. If there are caps with your throttle cable coming out of the top and it looks clean and neat...your TORS should be gone already.
5: Honestly, right now I wouldn't waste your money on bigger carbs. Stock carbs will run well up too 70HP and I promise you won't be reaching that until your ported or running a 4mil crank. I still run stock carbs on my Aggressive Dune Ported stock stroke and it rips hard.
6: Read answer 1
7: I've always ran 40:1 Klotz R-50. You may need to check your jetting and do a plug chop.
There are some great members on here, I'm sure you'll have some good mods to consider and everyone will have there opinion on your questions.
I would recommend calling a site sponsor on here to order whatever you need.....I always use Wildcard Racing and they are great people. But any sponsor will be awesome to work with, just personal opinion.
-Zach