For mechanics that work on Honda's, I need help figuring out what's wrong with my car?

Me and my dad recently bought a new engine for my 03' Accord and we installed the new engine and the car starts up but after a couple minutes of letting it run the engine will start revving and we can't figure out why. Also the shifter is showing the cars transmission is stuck in drive and has a flashing green light. Any automotive mechanics or technicians know why this is happening and how can I fix it.

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