Idle fluctuates after engine swap?

What engine was put into it? If from the same year make and engine size, did you hear the "new" engine run prior to the swap? Idle surge on a Honda is usually an issue with the idle control motor but it could also be a vacuum leak from a bad line or loose hose. I would start by using a can of starting fluid and spraying it around the engine when you first start it and see if the engine changes RPM when you spray in one area. Then look there for a leak. If nothing, then use a scan tool to run the idle relearn so the IAC position is reset in the ECM. If that makes no difference, I would swap the IAC off the old engine onto this one. To swap you just remove the electronic connector and the bolts and swap them around. Then do the relearn and see if it's cured.