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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 EFI

Haltech

Stock PCMMegaSquirtHaltech SportHaltech Elite 750Haltech Elite 2500Holley Terminator XHolley HP EFIHolley Dominator
Cost of ECM~$100 - $300 for tuning tools~$600$1,187$1,200 for ecu alone$1,950 for ecu alone$1,200 with harness and 3.5“ lcd$1,433$2,300
Cost of Wiring Harnesses Uses factory 3800 harnessextra $224 for premium harnessextra $255 for premium harnessComes with the 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 harnessWill need some modification or custom harnessRequires custom harnessRequires custom harness
Ease of useModerateDifficultEasyEasyEasyEasyEasyEasy
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 trickyTerminator X is a lot like HP EFI but with a few less bells and whistlesSimilar to Dominator but with less inputs/outputsDominator is basically the state of the art. Holley is very reputable
water-proof?yesnonoyesyesnoyesyes
Wideband auto-tuning supportnonono?yesyesyesyesyes
MAP limits for speed density tuning1.4 bar 22 psi for ECM's internal MAP sensor 5 bar5 bar7 bar
drive by wire supportSome PCMs yes yesyesyes x2
Transmission controlyes yesyesyesonly with “Terminator X Max”noyes
anti-lag / launch control built inno yesnoyesyesyesyes
CO2 controlno nonoyesyesyesyes
Boost by Gearno yesyesyesyesyes
Flex Fuel sensor supportnot with a 3800 PCM yesyesyesyesyesyes
Stages of nitrous control0 116 48
fuel injection outputs6 61-61-8up to 8up to 812 “peak” + 12 “hold” = 24 injectors
Ignition OutputsOEM 684 ground
Can expand with CAN IO Module
4 12v or ground PWM
Can expand with CAN IO Module
20 12v PWM
16 ground PWM
Can expand with CAN IO Module
Digital Outputsnone 28 0
Analog inputsnone 10204413 “multi-inputs” + 30 sensor inputs (0-5v)
injector stages for fueling0 4
Internal Data Loggingno yesyesnoyesyes
Known Odditiesoh boy, yes not potted
can't use external battery charger with ECU connected
can't use external battery charger with ECU connectedcan't use external battery charger with ECU connected

It's true, aftermarket ECUs are not cheap but they open up a lot of doors and remove a lot of the limitations of tuning the stock PCM. Tuning an aftermarket ECU is much more intuitive and much quicker than flashing tunes to the factory PCM.

If you are planning on getting serious with your build you're going to be piggybacking a lot of modules to give you all of the typical functions you would need while retaining the factory PCM. The costs of all of these begin to add up compared to using an aftermarket PCM that can replace all of these things so there's a good argument for just building the car with an aftermarket ECU right off the bat.

Factory tuning route - turbo stickshift drag car:

HPTuners or DHP $300 - $600
wideband $ 200
electronic boost controller $ 300
MAF Scaler (mini AFC) $ 160
WOT Box (anti-lag & no-lift shift) $ 220
LS style coil near plug (CNP) conversion module $ 160

Total cost if you added all of these modules would range from $1,640 - $1,340. If you went with just the basics: DHP, wideband, and MAF scaler you would stll be spending $660 and have a pretty archaic way of tuning your car.
An aftermarket ECU can eliminate all of these modules while also being much more user friendly and are much more extensible if you want go with some sort of wild inputs and ouputs in the future.

To use the Holley as an example, switching to the most basic Holley gets you built-in:
- wideband based fuel self-tuning
- boost control
- speed density tuning (Throw away your MAF)
- anti-lag / launch control
- run any coils you want to
- customizeable advanced tables
- customizeable inputs and outputs
- extremely fast reads and writes
- live tuning for things like fueling and timing
- expandable with Holley's CAN bus
- much much more