4.6 dohc in a fox

I'm doing a similar swap...4V swap w/Mach/99-01 Cobra intake single turbo...

Lets see if I can keep this in some semblance of order here...

Engine:
As complete as is possible to include all wiring/accessories
Engine mounts are basically irrelevant since you'll probably replace the factory ones with ES poly or something similar; if you want to use factory mounts, I'm pretty sure anything from '96-'04 will work-we'll discuss k-member in a sec

Trans:
You didn't mention if you wanted to go stick or auto...either way, you'll need to shorten your d/s since the 4.6 is set a little further back in the bay. You'll also need to fab up or purchase some mount brackets that move the x-member back to accomodate the trans mount.

Brakes:
Sorry to say you'll have to ditch your vacuum assist power brakes...you have a couple of options though-either hydraboost (get as complete as you can from a 96-04 V8 car) or you can go manual brakes. If you do, you'll probably want to modify your brake pedal to get a better pedal ratio to reduce effort...otherwise your brakes should be more than sufficient.

On your brake issue-the reason the pedal is so stiff is due to the larger piston diameter in the '94 MC...if you want to reduce pedal effort, see the above statement. Again, though, your current MC/booster will have to go for either a manual or hydraboost...

Chassis/suspension:
There's a couple ways to go about this; get a factory SN95 K and modify it to fit your fox (there are threads and tech articles about this) or you can buy one pre-fabbed to fit your car with a 4.6 (this is the route I'm going with a PA racing K...cost me about $300)

Fuel system:
Depending on your end goals, you can go a few different routes with this one. You can keep your factory tank and run a big pump, or get an '86-95 pump module and run a 255lph if you just wanna go stock or mild mods. You could get a later model tank like out of a 99-04 and put in a 2 or 3 pump hat, you could get the Aeromotive stealth kit...this is really up to you and how much you wanna spend. If memory serves the MKVIII stopped production in 98, so the fuel systems should all be return style...that makes things a little easier IMO.

This ought to get you started....hope this helps

Guess I should've asked...how much are you expecting out of this swap? Do you plan on modding the engine? Adding boost? Or just a cool cruiser?

As for making the harness work in your car, start searching for pinouts to the harness...you'll need to provide some power taps for the ECU, O2 sensors, fuel pump wiring, etc...it's not really difficult, but somewhat detail oriented, and you'll want a good multimeter to shoot wires and make sure you're getting power where you need it...do it right the first time and you won't have any problems. This site should help you out some

www.fordfuelinjection.com