This all sounds like it'll work out fine in the game universe! Downtime between when he's out of the Alaskan Academy and pulled in for Valparaíso can be explained exactly how they explained Raleigh's in the film: by not being explained at all really "yeah we let him wander off and work the highly dangerous wall for five years it's all good!"

Stacker Pentecost was probably the official who signed off on Mike's reintroduction to the program, though to what degree he knows on how far Graiman's experiments went, and to what ends, will likely stay an unknown area until if/when it becomes relevant. Having an unknown watcher in the Shatterdome should be easy enough, so altogether, everything sounds good to me.