So I'm almost certain the issue with my bike is the magneto/stator (I don't know the full difference), with a fully charged battery it will run for ~25-30 minutes then dies. No spark. Battery depleted. It's not charging.

I have 2 other bikes that need to be rewound, a GS750 and Jawa moped so I'd really like to learn how to rewind myself instead of spending ~1200 on shipping them out. Is it pretty much just document the specs on disassembly, use the right gauge replacement and insulator when you rewind? I tried searching but couldn't find many threads on this so any recommendations are appreciated, thanks!

What is the year and model of your bike? My 1973 RT3 also had a battery that would go dead after about 1/2 hour. The factory service manual noted that if you have a problem with a battery that doesn't stay charged you can unplug the green wire and plug in the white wire for a higher charging rate. It now goes much longer before running down. If your bike has this feature and it's not a daily rider it may work for you.

As asked in the previous post: What is the year and model of your bike?
Also, a couple more questions. When the bike is running is there AC voltage from the green wire or green/red wire coming from the magneto? Is the rectifier OK? Have you measured the resistance to ground of the green wire or green/red wire.