The CARB exemption that comes with the turbo kit is only good for one specific kind of engine/chassis setup. That's why you see kits certified for 92-95 Civics, but not 96-00 Civics- even if they'll work just as well on either configuration. Since you're swapped, you're deviating from that exempt setup- so you won't pass unless you grease someone's palms with some extra cash.
The B18 swap with the original OBD2 emissions hardware WILL pass smog if you go through all the proper channels, but not if everything's setup with the OBD1 hardware. You're removing (disconnecting) some of the car's smog equipment by converting to OBD1, so that doesn't pass.
If you want the car to pass, hook up all the emissions goodies (including ECU) that came with the car and make sure it runs without any dummy lights, then take it to the smog ref. Make sure all your turbo stuff is out of the car and not just sitting there not hooked up. They'll know something is up if you leave it in place. When you're done, put all the OBD1 crap back in and reinstall the turbo kit.
It's a pain in the ass, but at least you only have to do it once every 2 years in Cali.