If the engine and pump are "timed" as you say.....then it's just bolt it up to the trans / clutch / flywheel and go.
If you want to check your timing with the sidekick flywheel, you'll need to use the Acme marks on the sidekick flywheel.....IF it is an Acme flywheel that is......., to locate TDC.
If you don't know how to time an IDI vw diesel, you have much to learn [ first ].
The aaz should be a direct replacement into the engine bay, except for the oil cooler / warmer driver side engine-mount interference. This oil cooler / warmer mount / bracket is different between the 1.6 and the 1.9.
Jeff can assist you on this.