I have swapped the engine in my 1995 civic VX 5 speed (D15z1) with one from a 1998 civic HX (D16y5) that had a Continually Variable Automatic. I used the 5 speed and wiring from the 95 engine. I had to change the connectors on both the Intake Air Temperature sensor (IAT) and the Evaporative Emission Purge Control Solenoid Valve (EVAP) since they differed from the 95 wiring harness. They had only two wires each (95 and 98 versions). I swapped out the 98 injectors with the 95 since the connectors were different. The 95 distributor is close but won't fit on a 98 head. MSD makes a conversion connector so the wiring didn't have to be changed. The swap was rather straight forward. No mechanical changes had to be made.
I do have one problem I'm hoping the form can help me with. The Idle Air Control Valve (IAC) on the automatic version of the 98 engine has two solenoid control inputs (windings) plus a common. There are three wires in all. The 95 and 98 manual configuration is one solenoid control input (two wires in all). The engine seams to run fine but idles like crap. I currently don't have the (IAC) connected. As expected I only get one code in the computer, #14 Idle Air Control Valve.
I compared the 98 (automatic) IACV to the 95 (5 Speed) IACV. Each wire of the 98 is 20 ohm to common. The 95 is 11 ohms between the contacts. I tried both of the wires as well as the 2 connected in parallel. No luck! The idle is still surging. If I must replace it with a manual transmission version will it gist swap-out with the original one?    
Thanks
Bert  

Well for starters you used the harness for a 95 d15z1 auto on a 98 d16y5. That does not work. The d15 is non vtec and the d16y5 is vtec. Are you using the d15 ecu? If so that will not work right either. In short you need to use the whole harness from the d16 and the  ecu.  

YEAH SINCE THE MOTOR IS VTEC USE A Z6 OBD1 VTEC HARNESS AND P28 OBD1 ECU OUT A EG EX IF U HAVE THE PROBLEM STILL TRY SENSORS