I agree, it's a bit of a daunting process. I started with a TwEECer RT in 2004 and it's only today, in 2014, that I can honestly say that I can tune anything running the GUFB strategy. That being said, it's definitely one of my favorite pasttimes (datalogging, tuning, etc.) and I enjoy it immensely (although it can be very frustrating at times). I've retrofitted many vehicles with EEC-IV, including several friends' 5.0 Mustangs (an '84 GT and an '85 Capri). Tuned the crap out of mine with the KB Blowzilla. I retrofitted EEC-IV with EDIS8 onto my '79 Bronco with a 400M (Cleveland engine) and it runs perfectly.
More recently, I've jumped into EEC-V to inject the 408 stroker in my classic Mustang using Quarterhorse. Now that has been a major PITA. The issue there is that the freely available strategy is not comprehensive enough to build a great tune and requires paying for a good definition. And even then, I've had major issues simply getting the hardware to talk properly with the Quarterhorse. Having some TwEECers laying around, I decided to swap them in and have noticed that they work a lot better than the Quarterhorse. However, the TwEECer has a very limited payload and that is definitely a concern in EEC-V because of the much larger number of parameters you can/may want to datalog.
Anyhow, if you're spending the money on the tuning hardware and software, you're obviously quite serious about getting into tuning. The resources are available online via EECTuning, EFIDynoTuning, Corral, and many more sites and forums. Yes, there is a learning curve, but it's a heck of a lot fun.
'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.