HI Stephen,
Yep, I believe you are right the AFR's do flow better than the GT40P's but the New AFR's cost a lot more than the 2nd hand GT40P's and the GT40P's should be a lot cheaper.
As far as just changing the heads goes, I'm not sure it would be that great (for the $). The intake manifold (upper and lower) would probably need to be match ported and it would not be worth it as I'm pretty sure that manifold (NC) isnt the best. Not much point having hi flow heads if the manifold wont supply the extra air. If you decide to change the cam shaft later you may need to change the springs on the valves (further expense).
Most experienced engine builders seem to suggest that if you a planning an engine build you should:
1. Decide how much power you want.
2. Check that the block and crank can survive that power.
3. Decide which Cam shaft you will need to generate that power.
4. Build the engine to suit the camshaft.
The camshaft determines how much air and fuel goes in and out. That tells you how much head flow you need, what size throttle body, what size injectors etc. By following this method you will hopefully only have to build the engine once!
As was mentioned by someone else a fitted, working supercharger (with all other necessary mods for the supercharger to work properly) would not give any change from $10,000.
Stroking the engine will give quite a bit more power (than standard motor) but is also quite expensive since you will still need cam, heads, intake, throttle body, injectors etc.
If you dont want to get a bigger engine. Another option might be to purchase a ford with a motor that is already done up. Swap the motors over and sell the car again. If your lucky you might be able to do it for free. That way somebody else went through all the hassle for you.
Hope some of these ideas are helpful. At the end of the day its your car and your money so as long as you enjoy the mods its all good. Just do lots of research first.