you stole my idea!!!! i wanted a teskid block, high comp internals, and 03/04 4v heads with 98 cobra intake cams, a mach1 manifold and a t-56 in my car!
so far i have the heads and the trans, i need to source everything else.
i didnt read thru everything, just skimmed thru some of it. here is the run down of my research:
-the cobra 4.6 block will fit perfectly in the engine bay of your car
-if you get the teskid block, the 03/04 heads will work perfectly as well, just a simple bolt on
-the t-56 will bolt in directly to ANY 4.6 that fits in a mustang. if you get one off a cobra, you will need to get a dallas speedcal to make the speedo work, since the cobra came with an electronic VSS versus our mechanical one. also, you will need the install kit from D&D transmissions to make it mount up. you will need a shorter driveshaft: if you already have an aluminum one, you can get it shortened by 3/4" (i believe), rebalanced, and it will work. if you get the cobra driveshaft, you will need to get a special u-joint and swap over the flange from the GT driveshaft to the cobra driveshaft.
-to make the stock eaton work, you will need a lot of parts off an 03/04 cobra, much easier to make it an 01 cobra and get a KB kit for it, or find a parts car/donor car which will be hard to do.
-since your car has a return style fuel system, you will need to run 96-98 cobra fuel rails and the cobra fuel pressure regulator. these fuel rails will not work perfectly with the newer manifolds, they need to be slightly modified to make them work. you can get 98 cobra injectors to use, but if you go with a KB or Whipple, i suggest some 60lb injectors
-if you plan on keeping the wiring simple, you will need to get a 96-98 cobra timing chain cover, 96-98 cobra spark plug wires, and 96-98 cobra valve covers, or make the wiring complicated and convert it from the dual coil packs to the coil-on-plug design of the new cobras
here is what i would suggest you do if you want to go with a KB or whipple:
get the teskid block, forge the internals, keep the compression low, maybe 9:1.
get the 03/04 cobra heads, keep the stock cams on there since they are made for the blower (or get mach1 heads and get blower cams in there)
get the 99/01 cobra or the 03/04 mach1 upper and lower intake manifolds, with everything you need to install the heads as well (crossover tubes, radiator hoses, t-stat housing, belts, valve covers, etc)
go get a supercharger kit for a mach1 (or 01 cobra, depending on what manifold you are using) and install that.
doing it this way will avoid you having to get an 03/04 cobra timing cover, the front accessories, the supercharger drive accessories, and all that other good stuff. ive worked on taking the heads off a termie before, and trust me, that stupid crank pulley is not a fun job.