Aftermarket ECUs

Generally if you're going this route you probably don't need any guidance about how to do it. Here are a few aftermarket ECU options and some differences:

Megasquirt

Holley Dominator

Haltech

Stock PCMMegaSquirtHaltech SportHaltech Elite 750Haltech Elite 2500Holley Dominator
Cost of ECM~$100 - $300 for tuning tools~$600$1,187$1,200 for ecu alone$1,950 for ecu alone$2,100
Cost of Wiring Harnesses Uses factory 3800 harnessextra $224 for premium harnessextra $255 for premium harness$365 for universal main harness
Ease of harness install for 3800Plug and PlayRequires custom harnessPlug and PlayRequires custom harnessRequires custom harness Requires custom harness
Ease of useModerateDifficultEasyEasyEasyEasy
ReviewsGood enough for most peopleDifficult to put together, but a lot expandability. Pretty dated nownot great State of the art. Created in Australia though support can be trickyDominator is basically the state of the art. Holley is very reputable
water-proof?yesnonoyesyesyes
Wideband auto-tuning supportnonono?yesyesyes
MAP limits for speed density tuning1.4 bar 22 psi for ECM's internal MAP sensor 7 bar
drive by wire supportSome PCMs yes yes x2
anti-lag / launch control built inno yesnoyesyes
CO2 controlno nonoyesyes
Boost by Gearno yesyesyes
Flex Fuel sensor supportnot with a 3800 PCM yesyesyesyes
Stages of nitrous control0 1168
fuel injection outputs6 61-61-812 “peak” + 12 “hold” = 24 injectors
Ignition OutputsOEM 68
Digital Outputsnone 28
Analog inputsnone 102013 “multi-inputs” + 30 sensor inputs (0-5v)
injector stages for fueling1 4
Internal Data Loggingno yesyesyes
Oddities can't use external battery charger with ECU connected