High RPM at idle

[Dream240]

Hey guys.

Got a problem with my new 5-speed swap.
I got it running good. Only problem I'm having is the RPMs rise to 1500 when I slow to a stop. As soon as I stop the car, the RPMs jump up to 1500 and slowly fall to 850 and then it's normal.
This also happens when I put the car in reverse and begin to engage the clutch with no gas pedal, the rpms jump up.
I'm wondering if it hs anything to do with the auto ECU? Maybe it's still searching for the auto transmission and put it in 1st gear so that it's rady to take off again? I didn't have this wierd idle problem before I did the swap so I know it's related. Any ideas?

My other question is, should I swap out the auto ECU? And do I need to hook up the clutch pedal switches or can I leave them unhooked? Since one of them is already eliminated by the jumpered wires for the car to start, and I don't know what the other switch is for.

Also what are the side effects from running the auto ECU in the 5-speed swap? (if any)

Thanks.