First off, considering those GT40 heads are available off of 90-something Ford Explorers in the junkyards/u-pulls for cheap, unless those $350 heads are a pair straight out of the machine shop, new springs, totally reworked, that price is highway robbery. If you don't want to bother with a junkyard or spend a day pulling a set for yourself, you can find them in MANY places, like Craigslist. There is a junkyard fresh (LOL) pair on the Corral classifieds right now for $110 bux, and when that set is gone, there will be more to replace it. The thing is finding a local set to avoid shipping... They are out there.
As far as porting heads, it does work, you just have to be reasonably careful not to damage the heads if you are a newbie to porting. This is a hobby afterall, so if we can't do our own mods when the budget is tight, then we might as well not be in the hobby.
The stock intake will work with GT40 heads.
It sounds to me like you need to find a 96-97ish Ford Explorer donor and just buy the entire top end.
That way you'll have everything... GT40 heads, upper, and lower.
All you need after that is either an elbow to use your stock TB, or the small parts to swap over to a Fox TB.
(If you want to go Fox TB, grab the 65mm TB from the same Explorer!)
As for the E-cam, your experience might be different, but we don't like the way a cam acts in an SN.
Do some research on idle surge, the SN computer interacts with the cam differently than a Fox computer, and a different, larger LSA, cam might be a better choice.