Voltage drops and misfires. Need help!!!!

Ok, I have been looking everywhere for a answer. I swapped a Jdm odb1 p30 ecu b16a motor into my 98 hatch. First time. Had a few bugs but working them out. One I just can't seem to figure out though is a voltage drop and a weird misfire that is most noticed at idle. When mis happens voltage at battery drops sometimes to 11. volts. Not sure if the two are related but I was thinking that low voltage may be causing this. I have changed plugs and wire (ngk), cap and rotor, alt. rebuild, pulled wire harness and rechecked. There are no cel's. I have done a Mishimoto radiator Aem intake, Peak Performance headers, Obx twin loop muffler, Moroso oil pan and thats about it. Clutch, timing belt, water pump, and other misc. maintenance. I wouldn't think that it would need to be tuned on a dino yet but shop had told me that might be something that needs to be done.... They get $ for that you know. Anyways any help would greatly be appreciated.