RE: engine
Well, let's see. The cam profiles are slightly more agressive on the cobra engine, the exhaust maniflods are different, the intake is different, the oil pan is different, the flywheel is an 8 bolt piece instead of the 6 bolt that's on the mark, and a few nuts and bolts. But if you're just doing a swap it's pretty strait forward. I'm about to put a 97 cobra long block into a 95 mark viii this week. I have the new motor ready to go in just waiting on a couple of parts to bolt the tranny up and go back in. If you're wanting to add more performance the I suggest getting all the parts needed to use the cobra intake, headers, and a 3500 rpm stall convertor or something similar. These will all make a world of difference. These 4.6's cannot be bored more than .020 over as the cylinder walls are too thin. You have to have the block modified and a big bore cylinder kit installed. That kit alone is $1200 or more depending who you go with. If you aren't going to go too crazy then a stock cobra or mark viii long block will handle a decent amount of power. If you are going to add N2O or a blower then make sure you have a good tune. A good tune is the difference between a long running motor and a couple of rods hanging out of the block. Now if you're going with a 99-01 cobra motor then the differences are pretty drastic. You would need the cobra's accessories, or you would have to swap out the cam covers, the heads are different, the intake is way different, the cams are different, and the wiring is very different, also they have cop's (coil on plug) like the 97-98 mark viii's and that would mean using your cam covers or swapping to the cop setup...which isn't easy from what I understand.
Did I miss anything?