Andy

Man, my old hybrid was a CX, I couldn't wait to tear that motor out (I still have the head sitting in my closet, someone was going to buy it then never sent me any money). I'm guessing part of the problem is the stock CX ECU, it's only designed to make 70 hp on an engine with only 8 valves, so the timing and fuel maps are completely different than what your new 16v head needs. I would consider swtiching over to a '92-'95 DX/LX ECU and seeing what that does for you. The ECU's have very little value to their old owner and you can probably get one real cheap, make sure you get for a manual car though, an auto one will always throw a check engine light (it will just assume the transmition is failing to respond when it's simply not there). If you still have the old distributor, you might consider swapping that in and trying that. As far as I know, all D-series distributors are the same and should work fine. I'm assuming you've checked the timing and it's right where it needs to be.

To be perfectly honest with you, the gearing of a CX tranny is garbage. I don't know how many miles you have on your block and if the deck warped at all when the old headgasket blew, but I would consider sh!tcanning the whole shebang and go shopping for a nice SOHC VTEC D16Z6 from a '92-'95 Civic EX (or Si hatchback) and just starting with that engine as your base for the turbo. Shop around enough and you can probably find a complete, longblock/tranny/axles and ECU combo for less than $500 (maybe even from a local wrecking yard if you get lucky, people have wrecked a lot of Civic's over the years). It will give you a solid foundation for everything, the extra compression and performance of a VTEC engine and best of all, a VTEC tranny with it's more aggressive gearing. Longer gearing is desirable for a high boost, high hp buildup as your basically just not shifting as often, but more aggressive gearing = faster, traction limited (unless your planning to sleeve the block and run new internals, the shorter gearing is what you want). Just something to consider, I don't know what your budget is for this project and whatnot. I'd try the old distributor and see if you can find a DX ECU just to try (any buddies have civic's?) to see if you can get the other engine to smooth out.