1988 Honda Civic -- Idle goes up and down

I have a 1988 Honda Civic. I recently replaced the motor with a Japan Import. So I am guessing it has around 50K to 70K miles. It runs great but when I come to a stop the idle goes up and down. It is not a good steady idle. I have messed with the idle adjustment, replaced the spark plugs, and distributor, but still having the same problem. Could it be in the vacuum line. All are hooked up but I have heard that Honda's are notorius for have this problem after an engine replacement. Please help.

Thanks,
Shane