1. a/a= air to air, ambient air passes across the fins and cools the boost air. a/w= air to water, there is two ways of running an a/w setup. 1st way is for cars/trucks that are track and street. just like the supercharger guys on this forum, there is a heat exchanger, a water tank and then the actual intercooler itself that the air passes through. 2nd way, water tank and intercooler ONLY. no heat exchanger. this is for a track only car. the water tank is insulated and then filled with ice and water. ice water is about 32*. think about how well your boost air will cool down coming from the turbo and then passing through an intercooler at 32*. once the water gets warm, it has to be drained out and fresh ice water filled in.....thats why its for track only.
2.that will be just fine. i only used a little 3" before the turbo because thats what i had laying around. i would hold off on buying mufflers. i only have 2 cats and the turbo, no muffler and its QUIET. at idle and crusing it sounds no louder then a stock truck with a magnaflow muffler welded in. slight rumble, nothing more.
3. should be higher but how much is hard to say. your tires are larger then mine so heavier. but you have more cubes. 10psi on your motor and those tires i would expect 400rwhp ish.....but like i said, hard to say.
4. depends on the turbo you pick. my mustang runs t3/t4 hybrids so i run t3 flanges. my truck's turbo is a t4 so i run a t4 flange...thats feeding the exhaust side, leaving the turbo, again, depends on the turbo. some turbos use a flange, others use a v-band. the one on my truck uses a 3" vband.
5. what is that? is that a plain ol' x3 or is that some sort of tuning software? if its just the hand held x3, you cant tune the truck with just that. you need tuning software.

stock manifolds will work just fine.

for what its worth, this is the exact turbo i run http://www.ebay.com/itm/3-Performanc...ht_4111wt_1115 (didnt pay that much but thats the one) you can choose the exhaust ar, you want the .68, not the 1.0, it will spool faster. and its a t4 flange, so you would buy this http://www.ebay.com/itm/T4-Large-Fra...9#ht_500wt_896

and use this exiting the turbo http://www.ebay.com/itm/3-V-Band-FLA...ht_1959wt_1115

 

Plain X3 I bought from a guy who had custom tunes for a lightning on it. I plan on having that cleared and do 3 custom tunes programmed to it with the truck on a dyno.

 

on the trucks you can flip the manifolds and bolt them to opposite sides and do a front mount turbo setup.

 

haha master power turbos good luck!

 

Mp used to have a bad rep but they seem to have resolved the issues they once had