I took my 95 Civic EX sedan in for CA smog retest after I replaced SP wires, O2 sensor and catalytic converter and they said I now fail the RPM test at 25 mph on the dyno. I passed that part of the test before changing those things.
What can be causing my car to run at more than 3500 RPM in second gear at 25 mph ( I never paid attention to this before)?

 

I assume it is automatic. You need to adjust / repair the cable linkage between the throttle and the transmission. When you floor the gas, the cable tells the transmission to "kick down" to a lower gear and let the engine rev higher. On your car, that seems to be happening all the time evne when the gas pedal is not floored. That is bad for mpg and emissions.