In the future I want to upgrade my 5.0 to a 306 supercharged that will still pass emissions. Someone at MMS to me to go the new 5.0 route w/412 hp as it would cost about the same. So I see several people on this site putting 2v, 3v and 4valve motors in older fox bodies. Any thoughts on this?
There's a thread on the Fox 5.0 page that details the swap to a new 5.0, and there's other sources to find good info. I'm not really sure just where you're planning to get all the parts, but a new 5.0 with the FRPP supporting hardware runs over $8k...so, unless you're buying a powertrain from a wrecked car, I'm not sure how building up a basic supercharged 306 would cost that much...you can find used stuff all over eBay that would allow you to build up such a combo for less. BUT...
Swapping to a new 5.0 would be pretty swank, but if you've got 10 g's burning a hole in your pocket, it would definitely be one direction you could go. Another alternative, if you want to put a modular engine in there due to emission requirements, any 4.6 will help you in that regard-it doesn't even have to be out of a Mustang. If you scout around some, there were 4.6 4V engines (302hp) in Aviators...I've seen these engines go used with wiring for $1500-$2000. The older B head 4V out of a Lincoln MKVIII would also work, and I've see whole powertrains from those go for the same or less! There are two on eBay that I strongly considered just to have spare parts...complete engines with wiring and front dress for $850 or less. If you can't find one of those, the 3V engines from an Explorer or F150 could be pirated for a pretty decent price I bet. The only thing about 3V engines is finding one with a good wire harness or getting the FRPP stand alone kit so you don't have to cut and splice.
Up until I had a friend talk me into 4V, that was going to be the route I wanted to go...
Thinking of swapping to a mod engine is all fine and dandy, but if you're really wanting to drop it into a fox, start looking around for all the pieces you'll need just to put the engine in the car. You'll need a new K member, new tranny x-member (you'll have to weld in some mounts to make this work btw), shortened driveshaft (regardless of your transmission choice), you'll have to play with exhaust parts to make stuff fit together, have to source and adapt wire harnesses into your cars existing stuff, you'll have to change over to either manul brakes or hydraboost since the 4.6 is so externally large and you can't run a vacuum booster. You might have to change your fuel system depending on your goals, your cooling system will have to be modified or swapped over to 4.6 Mustang stuff...there's something I'm forgetting probably, but that's the big picture.