I am so confused right now as what the question originally was, and what were talking about....
So We all know the 96-98 cobras had the b heads, the 99-01 cobra had the C head w/o forced induction, the 03-04 forced induction with the eaton at 8 or 9 psi STOCK. Heads on the terminators were also C, difference between the 99-01 was the rods, and pistons.
You had the teskid and the... W... something that has starts with W block. the teskid block was made by that ferrari company for select marks and cobra's. Just have to run the block models. google it for more info I would normally state.
The Mach's in 03 and and 04....
Automatics 6 bolt crank, hyperneumatic pistons, forged crank, junk rods.
Manuals 8 bolt crank, forged pistons, forged crank, I forged rods.
The machs for auto and manual used the same intake.
The 98 cobra drivetrain and electronics was an "experiment" from what I read. Some problems with non interchanging parts between other years, cant exactly remember at this time.
the 3v's you could swap to that setup. but why, besides the hot rod cams that are ahhh loby, the gt hyperneumatic piston aspect kill me.
You can do the swap, but....go with navi heads turbo, 96-98 intake cam for the 20 degree longer duration, or comp stage 2 cams, port the shit out of the intake navi heads, the exhaust port on the navi heads are tremendous. holy crap is what I said when I seen the difference. For something a little more less seen out there, roll couple of gt35r built by hta so its more of a hta3786r or something, ets or out of australia there is a intercooler company, or va speed builds massive intercooler setups.
Lot of options, when it comes to 4.6's.
essentially..... GOOGLE THAT SHIZIT SON! haha