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.

If it's your CT3, then it should run without a battery and, if the magneto is fubar, it shouldn't run at all.

Yeah sorry its my 73' CT3 (I thought I added this to my autograph apparently not or possibly it was after the post). I'll do some more diagnostics and update this thread.

>If it's your CT3, then it should run without a battery and, if the magneto is fubar, it shouldn't run at all.

This is what confused me, could it just be the cables aren't insulated well and starting to short more with movement and heat?

I gather we're talking CT3.
Bit of a long shot but if its not charging & lighting/charging coils are fried, the ignition source coil used to earth within the lighting coils. I wonder if the two problems are inter-related if you're running out of spark as well as not charging the battery. In theory the two problems aren't related as battery isn't required for spark--but just saying!!. On re-thinking, does the headlight run good as it should straight from the mag--no faltering or irregularity.

If you need a rebuild, check with member DEET who does these as well as amazing new wiring harnesses and other great services.

It does sound strange to me.
HAve you owned the bike for some time and this is a recent issue, or is the bike new to you? If the later I'd check the ignition is correctly wired.
I've known people who've had this sort of issue come on and off with engine temp, so that could be.
Have you measured battery voltage with engine off, idling and normal run speed, or similar, to verify if it's charging. 
I wonder if measuring the resistance of the ignition winding before starting the bike and after it dies would tell you anything helpful?
I guess it could also be two unrelated things, no charging and ignition (somewhere) failing due to heat, I've heard of coils doing that as well as maggys.
What do you do to get it running again? Can it just sit and cool off?