i would leave the stock manifolds alone, put a good mid pipe on it, then the blower. if you do the exhaust after the blower it WILL affect the tune... when i had mine tuned the first time, i had just welded brand new high flow cats in. they were choking the whole system. after i drove on it for about 8 months and had it retuned, during the baseline run, the air fuel jumped up from 11.8 to 12.9, just from breaking in the cats... lol rwhp jumped from 357 to 390 as well...
whats really scary, is that i had an o/r h pipe swapped in there for a little while, which makes me really wonder what my a/f was at that time... the car ran AWESOME with the o/r h installed, im lucky i didnt cook my pistons...
thats my 2 cents.