hi, ive got d16y7 i pulled from my rear ended 98 civic and put in my blown 96 civic. the swap went fine but i made some upgrades such as 4-2-1 header stainless steel back to an apexi muffler with no cat, and cold are intake, msd 8.5 mm wires and some suspension mods. well the car ran ok but stumbled on acceleration and seemed like it was kinda loaidn up, but i figured the wires were burning hot.so today i put my old stock wires on the car and it ran great no stumbleing problems or anything, went about 15 miles and i was sitting in the car with it idleing and all the sudden it just started missing firing and back fire while driving, i got home and read the cel and it said misfire on cyl. 3, so i trying clearing and my auto pc started saying it couldnt and i figured it was cuz i changed my cap nd wires. now the the pc wont even read it but im not doubting the pc is junk. now the car only runs on 3 and 4 but not 2 and 1, i know by unpluging the injectors and 3 and 4 make the car die adn 1 and 2 dont effect anything. im thinking the distributor is bad but i wanna get feed back from the pros to see if it sounds like that or maybe a timing belt issue or a fuel issue. please help guys this my only car now....thanks alot...

 

Make sure your wires are in the right order, 1-3-4-2 as you go clockwise looking at the outside of the distributor cap. Check for skipped timing belt. Try a different cap and wires. The bottom of the distributor generally either works or it doesn't, it should not cause only certain cylinders to misfire. Listen to the injectors and make sure they're actually clicking. Next would be to check the compression, as you can blow the gasket between two adjacent cylinders and kill them both. Typically this doesn't have other blown head gasket symptoms like coolant in the exhaust.