Hondas are usually easy to work on.
Were the stock injectors for the z6 the ones you used or the stock injectors for your old a6 engine? Are you using a resistor box if they are the a6 ones?
Just a hunch, check your firing order on your distributor. Make sure that every plug wire is in the right spot on the dist cap. Also check the cap and rotor and check your spark. Inspect your plugs too.
Also check your wiring connections. Hopefully the connections were soldered, if not something could be shorting. My 89 crx wouldn't run right after I left my friend run the wire from the ecu conversion harness to the vtec solenoid. He ended up breaking a few wires when he ran it.