What would I have to do to swap an 03 Cobra engine into my 98 Mark 8?

A lot of work. Harness changes, mainly.

Ya... I need to make a write up, but in short:

Steering shaft mods to get past exhaust manifolds
Harness change, complete re-wrap with COP conversion, if applicable
Low profile intake change
Hood work or k-member shim
A chip or tune of course
Custom exhaust work
U-joint upgrades from additional torque created
Mounts galore, engine, trans, rear end, etc....