The easiest thing to do would be to put a Kenne Bell supercharger on the 'R. The blower is very similar to the Eaton on the '03 Cobra.
Kenne Bell made over 600 RWHP with a new '03 running his blower with stock manifolds, throttle body, and catalytic converters. He advertises these blowers for 5.4's. Although, I am sure it means 2V Lightening motors.
A friend of mine had a custom set-up done for his 350 sbc off-road car. Over 700hp on pump gas and a stock LT1 computer with reburnt chip.
5.0 mustang-had an article about a fellow with a 00R and a vortechsq-it was a modified 01 4vkit-i think they had to fab the bracketing and he ran a return stlye fuel system form a 98gt (this was before solutions to the returnless came out) with 8psi he put down 569rwhp and 509 tq. On an otherwise stock R. (oh he had a diablo chip too) And he got to keep that beautiful intake! as opposed to a kb setup.