new guy....few questions?

The '03 Cobra heads are different from the Mark VIII heads. Mark VIII engines mostly did not come with a forged crank. If I remember correctly the Mark VIII engine is a slightly detuned '96-'98 Cobra engine with some internal hard part differences.

You may want to look into a Kenne Bell setup for those '96-'98 Cobra's or a Procharger/Vortech/etc...setup.

I haven't doen the swap. So I can't offer any tips. I can though offer an idea on engine management. WMS. Western Motorsports in Canada makes a real nice plug in system that will easily run what you have and what you seem to be headed towards building. It's realitivly in expensive (around $1000 bucks) and everything you need to install, tune and run it is included.

the lincoln mark 8's were designed to run with an auto, and have cast cranks with a teksid block, you should upgrade the heads to 03-04 cobra's and add a KB if you want to