Time to open my notebooks from my swap research days...
But from a less technical standpoint...
"Better" would be for you to simply go with the snd Gen due to the transmission (given your car is already manual?) The cable tranny on the first gen would create a problem... sure you can get the cable to hyrdo conversion, but why all that if the price in the end is about the same as the 2nd gen.
96+ EKs have an added issue to be concerned with: OBDII which exists only in the USA - not Japan. As such a '96+ Civic wishing to install the JDM '92+ or newer B16A will have to use an OBDI ECU (JDM or USA pre-'96).