First off let me introduce myself. I'm Drill1, not a mechanic by any means but do work on simple stuff. I live in South Texas and work in the oil field. Just happened upon this site while trying to trouble shoot a problem I've recently encountered with my 89 Suzuki  Samurai.

This is my ranch ride where it has stayed and ran flawless for the past four years, until December when the motor locked up on me. So had another motor installed in it. It was the same motor as the one that was in it before. 99 Geo Tracker.

Here's my dilemma. Starter sounded rough when I first cranked it on after picking it up from the mechanic. He said the fly wheel needed replacing. But it started and ran like a champ. Well after a few more cranks it just wouldn't engage anymore.

So I replaced the fly wheel and had a clutch kit installed while the transmission was dropped. This is when I noticed an adapter plate between the transmission and motor about 1/4" thick. Well after that work was completed and the starter reinstalled same thing happened. Cranked a couple times then nothing. Sounding rough both times.

Question is, since the marks on the front of the fly wheel and front of the starter spline suggest that the starter is not fully engaging/reaching the fly wheel probably due to the adapter plate. How can I get the starter to fully engage? Is there a starter from a different vehicle that might work in this situation that will fit?

Adapter plate wouldn't affect starter engagement.  The starter and flywheel maintain the same relative location to each other, since the starter and engine are mounted to the same side of the adapter plate.  Starter gear was probably damaged by using it on a damaged flywheel ring gear. Try a new starter.