JDM 2.0 Engine and original ECU

[deanrocker]

I have a unique issue that I'm getting conflicting information as to how to address. The situation:
I own a 2006 manual transmission turbo Baja. The original 2.5 engine was replaced with a 2.0 JDM engine. It ran perfectly for a few hundred miles before the vehicle was partially flooded by hurricane waters, and hasn't run since. I cannot contact the mechanic to ask him questions, so I'm here instead. The car was flooded and I had to replace the ECU and some harnesses. I have removed all but a few minor codes ( P0851, P1152, P1153, P0137 and P0502). My understanding is none of these should prevent the vehicle from starting. Yet, it will not fire. I believe when I checked I had spark at all 4 plugs. I am spraying starting fluid into the throttle body and trying to crank, but it chugs, and never fires. The check engine light flashes quickly. All my grounds are good. The wiring to the ECU appears to be good.
I did notice some harnesses underneath the vehicle that were attached to the engine, but wires led nowhere. I think the mechanic just didn't use them when he replaced the engine.
My questions are:
1. Would the mechanic have needed to reprogram the ECU when he put in the JDM engine? The place that sold me the JDM engine says no, but different places online say yes. The new ECU I purchased was in a 2006 Subaru Baja Turbo MT. Same exact as mine.
2. Would any of the codes I have yield "no start" conditions?
3. What could be preventing the vehicle from starting?
4. What is the next logical step in troubleshooting? I could address the codes, but I hate to keep throwing money at it if it's never going to fire.

I'm happy to pay someone for good information. Would love it if someone wanted to walk me through some steps. Thanks.

[anarchy1024]

The part number on the flooded ECU, is that for a 2006 Baja or another car? I'd think that at the very least the fuel maps would need to be reprogrammed due to the different engine displacement. P1152 seems to support that theory: the ECU senses that the fuel mixture is too rich due to it using maps for a much larger engine. Probably shouldn't cause it to not start, though.

Do you know what car the engine was pulled from? What wiring harnesses did you buy to replace the flooded ones? Did you lay the new ones beside the old ones and verify they were identical? Not just connectors, but also the pin wiring with a multimeter (or at least checking the wire colours)? I don't think any of those codes by themselves would cause a no-start, but all of them together suggest that there are some significant differences between the new and original engines, and it wasn't just a drop-in replacement.

The unconnected harness underneath, are the wires going nowhere in both directions?

I'd probably start with first checking all the part numbers on the flooded parts that you replaced and make sure the replacement are the same. Then I'd put the two wiring harnesses beside each other and check that each pin on the ECU side is wired to the same connector/pin on the engine side with a multimeter.