i have a 1990 integra with b18a1 and 5 speed swap just intake and exhuast done to motor for now,when i run what i believe is a auto ecu it runs perfect with no problems or codes,however if i run a chipped pr4 obd0 5spd ecu it starts runs and drive but if i touch the brake pedal it dies but is still not throwing any codes or anything and starts right back up...could this be a ecu problem or maybe my alarm???? at a total loss

 

If it runs fine with the other ecu, then I would assume the new ecu would be the suspect

 

I suggest you check the soldering and look for any bad solder.