If the replacement engine came with the throttle module (ETM), you need to re-adapt the ETM - basically the Engine Control Module has to re-learn the throttle plate positions.
This process requires an OE diag. computer, so you either need to tow it to a shop who has VAG-COM or get a tech who has one and willing to go to your location to perform the adaptation.
Here is some info from the manual:
Adapting to Throttle Valve Control Module
The adaptation teaches the Engine Control Module (ECM) various positions of the throttle valve when the ignition is on and the engine is stopped. These positions are stored in the control module Throttle valve position feedback takes place through the two throttle valve drive angle sensors.
The adaptation must be performed if:
* the supply voltage has been interrupted
* the throttle valve control module has been removed and reinstalled
* the throttle valve control module has been replaced
* another engine has been installed, and another throttle valve control module along with it
Special tools and equipment
* VAG 1551 Scan Tool (or VAG 1552 mobile scan tool) with VAG 1551/3 cable
I hope this will help.
Zee