I have solved my issues! In case someone ever encounters something like this, I will detail what I tested and how I solved said issues.
The issue was, the engine would not rev out completely. It ran fine, no smoke or anything but just wouldn't revv. All of this started happening after a very hot day of sitting in traffic.
Things I checked, compression, valve adjustments and timing. All of these things checked out and it seemed the only remaining items would be either carbs or ignition. Having just rebuilt the carbs and having it running supremely well, carbs seemed unlikely. I checked for any vacuum leaks, and aside from a bit of air leaking at the throttle blades, all was well.
I then tested the voltage while idling. Bike idled at like 11 volts and when revved would not pick up voltage. ALRIGHT, now were getting somewhere. I took off the stator cover and tested the stator. I un-clipped the stator plug from the rectifier which revealed some melted casing and really corroded connections. Although the stator passed all the tests outlined in the link provided below(*), I replaced it anyways to get rid of that nasty plug. I found a spare engine on craigslist with the stator and rotor for 75 bucks. Next I tested the rotor, between the two copper ? rings, only around 0.1-0.3 ohms. Its required to have around 5 ohms for proper operation. SOO, replaced the rotor. After having to beat the S%^t out of the bolt holding the rotor on, I got it replaced and all reassembled.
I did notice while I was tinkering that one of the coils had some cracking on it. I decided to pick up two new coils for 40 bucks on ebay (probably cheap off brands but whatever), and replaced the old cracked ones.
After buttoning it all up, I started her up and checked the idling voltage. It was ~12.5 volts idling, and 14-15 while revving!
Took it for a test ride and it pulls nicely through the gears again!
Here is the link which contains much useful information on proper charging system functionality and testing.
(*)
http://www.cb750c.com/publicdocs/charging_system/genesound_charging_system.html