If you are doing swaps, you should wait until you have swapped all the electronics before trying to start the engine. Because the original ECU was meant to operate in a different environment than where you have put it, you may have operational issues until you reproduce the original operating environment or modify the programming in the ECU for the current environment.
When you are done, at best, you will still have a compromise solution. The better approach is to go to an aftermarket ECU like an MS3Pro. If you do, I recommend you use the Plug and Play (PnP) variety they offer. When you have finished the installation, take the finished car to a dyno shop to get properly tuned. If you choose to use an aftermarket ECU, use the MAF-based tuning model in the ECU. Do not use the Speed Density Model. The Speed Density model will require a retune for each subsequent modification you make to the engine. The MAF-based model will not.
As you already know, OEM system components come with impressively large price tags. The price tag on the MS3Pro is $1499 — with tuning and data logging software. You will easily exceed this number by attempting to use OEM electronics and aftermarket tuning software. Additionally, you will experience problems like you are currently wrestling with but, without the control and programmability of the aftermarket ECU! Pick your poison.
When you are done, at best, you will still have a compromise solution. The better approach is to go to an aftermarket ECU like an MS3Pro. If you do, I recommend you use the Plug and Play (PnP) variety they offer. When you have finished the installation, take the finished car to a dyno shop to get properly tuned. If you choose to use an aftermarket ECU, use the MAF-based tuning model in the ECU. Do not use the Speed Density Model. The Speed Density model will require a retune for each subsequent modification you make to the engine. The MAF-based model will not.
As you already know, OEM system components come with impressively large price tags. The price tag on the MS3Pro is $1499 — with tuning and data logging software. You will easily exceed this number by attempting to use OEM electronics and aftermarket tuning software. Additionally, you will experience problems like you are currently wrestling with but, without the control and programmability of the aftermarket ECU! Pick your poison.