1994 Prelude High Idle in Gear only

Hello, I have a 1994 Honda Prelude Si with about 50k miles on it. Last week I swapped out my 211k mile engine and automatic transmission due to a cracked block with a used JDM engine and automatic transmission with about 50k, which run great btw, anyways, my problem was I have a high idle only in gear, which would be Drive or Reverse, in Park or Neutral the idle would be normal, sitting around the 850 mark, when I get into gear on a cold start the intake would make a loud sucking noise and the idle will climb from 850 to about 1300 and stay there, at operating temperature when doing the switch to park to gear the idle would go down like it’s supposed too, but as soon as i touch the gas pedal the idle will climb to 1300 and stay there until I switch back to park or neutral, on my old engine the car use to surge in gear sometimes at a stop, that was annoying, hasn’t done it with the new engine and tranny yet, though. Another thing is when I barely touch the throttle the idle will climb on it’s own to like 1300 and then I can hear a “pop” coming from the intake, then the idle will go back to normal, also at operating temperature going low speeds lets say in a parking lot I’ll be stepping on the gas a lil then I hear that pop from the intake and the rpm’s will slowly go back to like 1k, I can describe it like the transmission shifting but it really isn’t, when going accelerating and the rpm’s are climbing and if I let go off the gas the rpm’s will dip to like 1k and quickly come back to like 1800 or so. It all started last year when i took my old engine to get serviced for a timing belt and water pump, when i got it back it ran worse than before and the throttle had to be kept open to prevent the car from stalling, changed the intake gaskets and the throttle can now be closed fully, he also told me to change the throttle body and IACV, got used OEM ones and put them on and still nothing, I noticed he messed with the throttle screw, I tried another used throttle body that had a still sealed throttle screw, I tried another IACV, adjusted the FITV, bled coolant, sprayed carb cleaner on vacuum lines and still nothing, it’s still doing it even with the new engine and transmission in the car, I did use my old intake, cause the new one was different, any ideas? I can’t get it smogged until I fix this problem, thanks in advance.