You guys are on the right track, sort of. The Jaybird is actually the programmer that allows you to flash F3 chips, which would be the long term, more permanent solution. There's lots you can tune to improve the performance and efficiency of a 5.0L, even if it's mainly stock. You can adjust cam timing, spark tables, control e-fans and A/C, turn of emissions equipment, etc. While it's true that you'll be able to leverage your newfound tuning ability more with a heavily modified combo, it should be understood that the stock calibration of the EEC-IV was a compromise to suit a wide range of cars adequately, not precisely.
'89 5.0L LX hatch: all 90mm 2.2L Blowzilla Dart Iron Eagle 306 @ 8.4:1, ported Vic Jr heads, TMoss ported GT40 lower, Deka 80# injectors, EDIS8, GUFB-A9L2-Moates tuned, Tremec 3550, 3.31 gears w/31-spline TruTrac
'66 GT 2+2 Fastback: carb'd 289, Canfield heads - EFI transformation pending
'71 Mach 1: totaled - R.I.P.