Do I have a head problem

a lot of guys that swap motors keep their stock motors around, just to have a spare in case something breaks. try the atf trick first. it's a hole lot cheaper than rebuilding the whole engine and if it works, you saved yourself a lot of time and money. if it doesn't then you only lost a few dollars for the atf. the d16z6 should bolt in fine. what model is your civic? unless it's an HF or SI, you'll have to rewire for four injectors or buy a wiring harness from hasport. you'll also need the SI ecu and an rpm activated switch for the vtec or an aftermarket ecu such as zdyne or hondata. the tranny from the z6 won't work in your car. it has a hydraulic clutch, and the 4th gens have cable. your stock tranny will bolt up the the z6 block. i'd go with the z6 rather than completely tear into your stock engine unless you have an SI, then i'd build a mini-me. slightly more powerful than the z6, but that's a whole different story