I think everyone hit it pretty close to what I was gonna say.
The 03/04 is bad ass as all hell but if you only want 400-450 rwhp the better bet would be the 98. The cast iron 03 will be over 650lbs on the nose of a car with bad balence already. The Teksid will be 200lbs lighter and is a better block. If you buy the 98 and pull its engine/computer/harness then you will have all you need to do the swap. You can part out the Cobra for more then enough to cover the cost of an ATI with intercooler and pump down 425rwhp with no problem. I would suggest getting an AJE or MM K-member as well to help keep the car balenced. Also, dont disable the IMRCs on the modular cause they help alot and by switching the new comp over you will still be able to controll them.
Now here is the fun part. The Teksid block and 96-98 Cobra crank can handle more power then you will ever want to throw at it. So down the road if you decide 450ish (the limit for the rods/pistons) is not enough then all you have to do is get some forged dished pistons and some forged rods, turn the boost up from 8psi to 16 and put down well north of 600 rwhp.
On a Fox with a good
suspension you could pull high 9s with the A/C on
EDIT: BTW, the 4.6 N/A with long tubes and all the bolt ons will only be good for 315-325 rwhp at best. They do love boost though! The KB is my number one choice as it makes the little engine pull like a big block giving you over 500 rwtq at just 2100 rpm
Down side is they are $1000 more then the intercooled
Vortech/ATI kits and they dont have an intercooler avaliable for the "B" heads
You can use a meth kit but I hate having to constantly fill another tank. Without an intercooler the twin screw will never make the power that a centri can without hurting the engine.
The trans will hold 450+ as long as you are not doing constant 4K+ drag strip launches.