While my engine is running there is a skip/jump

I cant tell weather its doing the intake, compression, power or exhaust stroke. Any idea what that could be? The motor was just rebuilt and I was out test driving it. I shut the engine off then started it back up and it would run smooth then jump, run smooth then jump and it keeps doing this in park. When I put it in drive and I accelerate I hear a popping noise when I come off the gas and let it coast the popping noise backs off but the engine is still jumping. I don't know whats going on. Any suggestions?