Hondata doesn't do anything to the trouble codes, what ECU do you have? Someone is full of shit.
If you're using an OBD1 ECU, you'll have add wires to jumper out the codes, but after you do that it's like any other OBD1 car. It's easy to do. Hondata has nothing to do with it, unless whoever chipped the ECU did it wrong and that's why it's in limp home mode. You should be getting a solid CEL if there is a problem with the Hondata box, chip, or the chipping itself. If you want to get the Hondata system out of the equation totally, unplug the Hondata box and cut (or remove, depending on what the chiiped used) jumper J1 if you have a OBD1 ECU. The ECU will then run off of the stock program. If you have a OBD0 PR3/PW0 ECU, you will have to have the stock chip that was removed from the ECU during chipping. As a start though (for OBD1 ECUs) add the wires for the CEL and the DLC jumper and go from there. Good luck..

You're running in limp home mode for some reason, that's why it's running rich and rev limiting at 4k. Those are the failsafe defaults.

By the way, did it just start doing this after working fine, or did you just do the engine swap, or get the Hondata unit, or get a new ECU, or change some other major variable, etc.. ?