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I plan to get a complete 06 accord as a K24 donor complete with 5 speed manual and ECU. Should I get the 06 accord operating system or the kswap one? Will it be possible to setup this ECM for a cable throttle body vs using the DBW?

You'd need an 05 Accord ECU, 05-06 RSX, or SWAP ECU for cable throttle. The unit is the same KTunerECU R1 either way.

So is the main reason to get a different ECU to avoid the drive by wire? Have others been able to swap in a drive by wire throttle body?

Will the 06 accord harness be mostly plug and play with the older ECU?

To be clear you are recommending that i get a Ktuner swap ECU, do i need to provide a donor ECU or is this new hardware?

You can get any of the supported ECUs listed on the Swap application page. To add DBW you need to add a different pedal assembly and other things. On a DBW harness you will need to add wires and make other changes. It's on you to choose what route you want to go.