H22ek4

the car is a 96 civic hb and the motor is a 98 jdm h22. the problem is that I got the car to started up today but for some reason it would only stay on if I use my stock civic ecu, but when i use the p13 with obd jumper, the car would start and shut down, it would stay on for about 2-3 seconds then it would just shut down, its seems that the idle is not stable and there might be a vacumm leak or would it be a bad ecu? I bought some vacumm caps to plug some of the lines up but don't know which one to run or which to plug up. also which clutch hose did you guys used? the prelude clutch hose wasn't long enough, so i had to take the civic hose and connect to it but it is leaking. Also would it be safe for me to run the stock civic ecu for about a week or so or it cause the engine to run lean?