My experience with blown 2V's only includes centrifigul blowers and 4.6's. Of course the heads are almost (if not totally) identical to the 5.4's.
From the builds I've done, I've seen HUGE gains with boost-specific cams. I mean, to the tune of 50-60 HP increase from adding blower-cams over stock cams. Don't rule out a quality set of cams to the mix. It's an easy job, and well worth it.
Intercooling is a must IMO. I ran these on more than one car cxracing.com: 31x12x3 inch Universal Intercooler + 3" Piping Kit For MUSTANG 3000GT SRT-4 with great results!!
Of course, if you're going with a roots-style blower, you'd just run the heat exchanger that sits under the blower - again, I'm just thinking about centri-blowers.
Also, the best driveability came from HPX blow-thru MAF's VMP Tuning - Buy Ford SCT & GM Custom Handheld Flash Tuners Performance Economy Towing: HPX 05+ Slot Style MAF Sensor.