I recently swapped D16y8 bottom end and trans into my 99 Civic d16y7. The previous motor broke a rod. I had the head decked, leak tested, cleaned, and valve seals replaced and I recently put it back together when the car is cold it runs good but after 10 or 15 mins I hear chatter from the top end that's noticably different from when it first started and ideas on what to do now?

 

You appear to be running a P2P ECU with a D16Y7 head atop a D16Y8 block. If correct, you need a P2E ECU.