I have some 4.6 questions.

1: Yes you can use a 4v lower- Easy swap if doing romeo 2v but a windsor 2v bottom can be used but have to fill some front cover holes etc IIRC (I'm no windsor expert). But you may make more power on a NPI bottom end depending on rules.
A: what year cobra is the bottom end? Not all are the same.
2: 4v heads flow better out of the box. 2v PI heads are better then npi heads out of the box. Ported npi or pi seem to make similar power (there is multiple trains of thought on this one, kind of a bag of worms)
3: Call Todd Warren (Apocolypse performace) for cams. MHS does a good job too. A properly spec'd aftermarket cam will wake up a 2v or 4v combo.
4: 2v ones are all the same. If using 4v stock mach 1 headers are supposed to be factory ported/massaged for better flow.

Cheap, fast, reliable. Pick two. Stock short block rods from anything but a terminator (03/04 cobra) are going to be your limitation. But if NA then they won't be an issue. If trying to keep factory stock stuff a NPI short block with pi heads and some cams will net the best compression ratio and power with stock parts n/a. Don't fear the gear if staying na.

If boosting you'll want a terminator bottom end to really make power. 400-450 seems to be the sweet spot for anything not terminator rods. (Yes some make more power, most don't - i've windowed a few in the 450 range)

More info on the rules will help us be more specific.

If restricted to ford parts I would stick to 4v stuff. 03/04 Mach take out engine would be best bang for buck stock along with the stock manifolds (unless you can run a terminator setup). Get some 96-98 cobra cams along with a lid spacer. Stock TB and MAF is plenty on the 4v stuff.

Mixing and matching a 96-98 npi short block with 02-04 2v heads would net decent results as well. 4v manifolds/intakes don't fit 2v stuff. Upper Intake elbow and stock throttle body/maf can be a bit restrictive.

If having to stay 2v look for a 96-98 lower end NPI engine and mate with 02-04 PI heads/cams. That will be best bang for buck using stock 2v parts. You don't need the strength of the 4v bottom end with a stock 2v setup. You want the flat top pistons of the 2v NPI engine vs the dished 03/04 termi pistons. The rest of the 4v stuff has the same limitations as a 2v rod/piston wise.