99 civic ex with jdm zc sohc non vtec

Hey guys new to this site and threads. Well i have a 99 civic ex ((originally vtec)) with a jdm d16zc sohc non vtec motor and ex 5spd tranny and is giving me a couple of problems. First off everytime i start my car up it idles so low that the car would want to die and transmission shifts very rough and jerky. My car sputters all the time like it has two step or something.

All the wiring was done correctly and correct ecu is being used. What strange is that when i run the original ecu the car drives perfect and shifts smoothely only problem it has is an idling problem and wont pass 5500 rpm because i have no vtec obviously. But when i run the non vtec ecu which would b a p2e i get all these problems..

Do i have to change my engine harness to non vtec or is it a more serious problem.any help would b greatly appreciated!

Motor is a 96-99 jdm zc sohc non vtec obd2