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

Holley HP EFI

Haltech

Stock PCMMegaSquirtHaltech SportHaltech Elite 750Haltech Elite 2500Holley HP EFIHolley Dominator
Cost of ECM~$100 - $300 for tuning tools~$600$1,187$1,200 for ecu alone$1,950 for ecu alone$1,433$2,300
Cost of Wiring Harnesses Uses factory 3800 harnessextra $224 for premium harnessextra $255 for premium harness
~$700
Can buy as a kit
>$700
Harnesses sold individually
Ease of harness install for 3800Plug and PlayRequires custom harnessPlug and PlayRequires custom harnessRequires custom harnessRequires custom harnessRequires custom harness
Ease of useModerateDifficultEasyEasyEasyEasyEasy
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 tricky Dominator is basically the state of the art. Holley is very reputable
water-proof?yesnonoyesyesyesyes
Wideband auto-tuning supportnonono?yesyesyesyes
MAP limits for speed density tuning1.4 bar 22 psi for ECM's internal MAP sensor 5 bar7 bar
drive by wire supportSome PCMs yes noyes x2
Transmission controlyes yesyesyesnoyes
anti-lag / launch control built inno yesnoyesyesyes
CO2 controlno nonoyes yes
Boost by Gearno yesyes yes
Flex Fuel sensor supportnot with a 3800 PCM yesyesyes yes
Stages of nitrous control0 11648
fuel injection outputs6 61-61-8up to 812 “peak” + 12 “hold” = 24 injectors
Ignition OutputsOEM 684 12v or ground PWM20 12v PWM
16 ground PWM
Digital Outputsnone 28
Analog inputsnone 1020413 “multi-inputs” + 30 sensor inputs (0-5v)
injector stages for fueling1 4
Internal Data Loggingno yesyes yes
Known Oddities can't use external battery charger with ECU connectedcan't use external battery charger with ECU connected