A friend of mine has a similar setup.... '97 JDM B18C(GSR) running off the JDM P72 in his '96 hatch. The scanner at emissions testing showed "communication error". After looking around around under the dash we found out that the place that did his swap simply didn't hook up the wires to the port. If that's what you meant by "doesnt read anything" then I'd check that first. A simple test light will show you if that's the problem. After we connected the lines to the ECU he went back to testing the next morning and passed with no problems.

There is also another possibility.... (if you read between the lines a little on my post) if the scanner can tell that it's a JDM ECU it may be programmed to block communications or simply not work. (ie "doesnt read anything") To make sure that JDM ECUs can not get through inspection.

Autozone and places like it offer a free diagnostic check, which can be sued to confirm your port works. Better to go that route than to fail testing again. I know around here emissions testing gets more difficult and can result in your being tested more often if you fail more than a few times.