Tracker's 2021 literature shows several kicker options, and they are all extra long shaft. I don't know if the motor mount came with the kicker package, or if it was standard on the boat. What is further unknown is what they did in the 2000 model year.
Performance wise, the engine can be mounted either port or starboard. Often times a stbd. mount will interfere with the steering cables of the main, so a port mount is needed. If location has no issues, a stbd mount is preferred. If you ever want or need to tiller steer it, that will position the tiller in the right place.
If you don't already have a mount, buy one and install it first. Then measure the distance to the bottom of the boat. The prop must at least be below the boat. Position of the AV plate is not of any concern, per se'.
If you bought the package from Tracker I'm sure they would provide the correct prop. Since you are totally after-market, and since little kickers have a limited prop selection, just buy the lowest pitch prop available. Don't worry about rpms - there aren't enough options to be able to dial-in. Some prop catalogs might call it a "Sailboat Prop". One of my boats currently runs a Mercury 4-stroke "Sail Pro", which came factory setup with the best prop and even an internal generator.
