Wow, a massive undertaking at best and I wish you all the best with your project.
Feel free to use any of my work you wish to and if I can be of any assistance at all just shoot me a PM as that's always the best way to get hold of me.
Just a few ideas that may make building such a project a little easier IMHO:
List your questions on templates and I can help answer those. If I were you, I'd create each league as a separate template.
MLB
AAA
AA
etc.
Templates are great as you can mix and match any of them at will, anytime you want and then create a quickstart without worying about team and player ID problems as ootp will auto adjust those upon import without interfereing with any existings ones.
If you don't know how to manipulate players, stats, etc. in a spreadsheet, it's time to learn and it's also a tremendous time saver. Especially the vlookup and concatenate formulas as they will be your best friends.
I use Apache Open Office only as it's free. I can teach you all you need to know on how to use it with ootp.
I use it to create the games schedules and minor league stats to send to Markus each year. I also used it to create my NCAA D1 template for 2013 which has all real teams, players and stats.
Looking forward to your progress updates