The problem is the hybrid conversion harness contains the 'E' ecu connector and its pinned for 02-04 ecu use and not for 05+ ecu use, such as what your Ktuner RAD ecu is for.

And unfortunately, there's not a lot of support for using 05+ ecu + wiring use in a 90's kswap chassis's. You typically have to manually rewire an 02-04 harness and conversion harness to 05-06 rsx wiring/pinout spec.

 

Any idea how difficult that would be? I have experience with speakers and subs. Would it be easier to simply get a different ecu?

 

Depends on how well you like to be in repinning hell if you wanna stay 05+ spec. There should be youtube vids on how to depin/repin a k-series ecu connector.

Yes, bumping down to 02-04 wiring + ECU will make things a LOT easier.

The only annoyance I forsee is a possible speed sensor situation on the transmission. Depending on which transmission you're going with, if you're using the accord trans those typically run a high frequency CSS (not a low frequency VSS) and this will require a VSS converter in order for the 02-04 ecu to receive a vehicle speed signal so your speedo and vtec to work. Ktuned sells a vss converter. This wont be an issue if you have an 02-04 spec transmission that uses a rear mounted VSS (such as an 02-04 RSX or 02-05 EP3 trans).

your mount kit will need to be changed up as well if you're using an accord trans as they don't share the same mount bolt pattern as an rsx/ep3 transmission case.

 

in this case you want a 02-04 ECU (and loom). The VSS to CSS conversion business is at times troublesome, you need a converter = $$$.
On the engine loom the main difference regarfing compatibility is the crank sensor. You need a k24 crank sensor and rep in the connector as their pinout differs.