It's not so bad, but you have to either increase combustion chamber size (by larger/layering head gaskets or head work) or run very low boost. If you upgrade the fuel system, you can run boost safely, but it's really a teetering act. If you f' it up, your motor will not survive. Those blocks are stout as hell, though. 1,000HP, easy. If you can get a cheap forged rotating mass from a Cobra (or even the motor) and you're serious about making this thing fast, that's what you should do.
You want 400HP N/A? Cams. That's the only way. However, camshafts for a 4.6L Mod motor are expensive as @%$#! You could try to stroke it, but that's not cheap either. Basically, you need more flow than the stock intake and heads can provide, plus once you hit about 320HP, your injectors (which run at 19 lbs/hr) won't provide enough flow at nominal pressure to support that power.
Regardless, there is nothing you can do to that motor that will be cheap. Injectors are probaly the cheapest thing, because they cross over from the 5.0HO. Power = money. That saying is never wrong, and you need to determine how much power is worth to you.