the stroker 4.2 will clear the stock hood, because your intake will not change, even if you get the SSX intake from super six motorsports (eventhough I don't think they have 99+ intakes yet)
The best tranny, the one you have, the T-5. No need to swap the tranny unless you blow the 4.2 which you still should be ok with your stock T-5. If you want or need to swap the tranny and want to stay manual, price wise find a T-45, if price is not a option a Tremec 3650, or a T-56 if you want a 6 spd. But the T-5 should be just fine for now, don't have to waste money on something you don't need.
on an '02 v6, i don't beleive he has a t5, i'm not sure though, someone correct me if i'm wrong. and it'd be a pain to get the t56 to bolt up to the 3.8/4.2.