Uncontrolled throttle response

2003 Honda what? With which engine and transmission?

Okay, that sounds like an interesting project. From your description it sounds like the injector flow rate is higher than required for this application. It flows so much extra fuel that it is like you are at full throttle. You need the flow rate of a tiny perfume dispenser but the current injector is a garden hose.

What did the EFI unit come off of? I suspect you will need to lower the fuel pressure or find a lower flow rate injector, or find someone who can remap the current ECM to work with that engine or more likely a combination of the three. Lower pressure will reduce flow but the lower pressure will not atomize properly.

You could also look at the resistance of the current TPS between 0% and say 5% and see if you can stretch that out using a different resistor.

What did the EFI system come off of? I've never seen a fuel injected engine under 200CC or so and those are on a lawn tractor.
From your description the entire system is able to flow far more fuel that the engine can use. That means you need to figure out a way to make it flow less fuel.

That is a huge range for one kit to cover. Air+ fuel increase rpm. Ideally you want the throttle to be around 75% at the engines torque peak. I would say the throttle body and injectors are both larger than needed. Does the maker of the kit have a support line? They might be able to point you to a particular setting or programming curve to use for the smaller engines.