2) The difference of effect between 1 ST and 2 ST on a trainee not being pulled at the end of games is very limited.
If this is true, then it is because you are using CPfDC instead of SFDC. Pitiful Stamina (2) is absolutely enough to get 48+ with a lot of tactics combinations, using SFDC. Maybe not with RnG+FCP, I haven't tried that combo yet.
If your objective is to get a player 48 minutes in a single game, SFDC is the optimal choice.
3) Even if I trained him to 4 or 5 stamina (like Sid does when he gets trainees), would have this prevented him from fouling out?
Probably not. Experience, matchups and tactics plus aggresiveness would also need to be considered. But training him once in stamina would have probably allowed you to play him 48 minutes in the games where he didn't foul out, utilizing SFDC. 4 or 5 stamina would help his contribution to match ratings, but isn't necessary to reach 48 minutes.
are you sure you are prepared to manage a team with many 8 and 9 stamina players?
Yes, but if it happens it will be because I purchased them at that level, not because I spent 3 weeks training stamina for players who didn't need it to reach 48 minutes. I've trained Stamina one time in roughly 2 seasons, in a week where I had only 2 games.
Your willingness to play trainees a full 48 minutes should make training easier, not harder. The effects of GT is something you can plan to avoid,
or you can use it as a guaranteed 11-13 minute block for anyone that needs it. I find GT to be a very useful tool for balancing trainee and non-trainee minutes alike.