Air conditioning takes a long time to kick in

Sounds like you missed connecting a sensor? You should recheck every connector.
You could remove them and check to make sure the pins are not bent or pushed in.
And make sure they are securely fitted. It is working at times, so you know it's not the compressor.

 

Or hooked up wrong?
If a wire is pinched, and grounded, it could be giving the computer an incorrect reading.
Telling it that it is colder outside and that's why it doesn't come on until later.

If everything was working correctly before replacing the motor, and not after, then it's a good chance
that something is not connected, connected correctly, or a pinched wired, or a sensor or harness was
damaged when removing or installing the engine.

 

Are the condenser fans kicking on? At a stop, you should be able to hear them immediately when the a/c button is activated. I'm thinking it's only cooling while driving due to the air flow passing thru the condenser.

 

Check connectors, fuses and relays. Probably overlooked the connectors during the installation.

 

You're welcome. Hopefully, it's just a connection. And not something previous.
Do you have access to techstream?

 

You should use it to check the ac. It could tell you what the problem is, or point you in
the right direction.