After more research and digging on this bike, I determined that the timing was incorrect after the alternator / stator replacement mentioned above. Through the service manual, I was able to determine that the ignition system does NOT have adjustable timing via a distributor and instead functions by taking into account various sensor data including the pulse indicator (signal generator) which sits inside the clutch / alternator housing and is replaced with the alternator - since the pulse indicator was the only thing in this equation that had changed (aside from the alternator which wouldn't cause the strange timing issue), I removed the new by cutting the wires and put the old one back on and the bike ran great, first time.
I think ultimately the issue here was related to reverse polarity on the wires of the new signal generator and switching them outside of the alternator cover instead of stripping them off inside the housing and allowing the wire coating to be exposed to the oil, my issue would have been resolved as well. The best I can tell, if it's a non OEM part - they're very generic for different motorcycles and on some brands / models the polarity will be reversed of what it's originally wired for. Hopefully this helps someone else because I spent an outrageous amount of time troubleshooting various systems including a carburetor rebuild!
I'll also leave you with the below information describing the ignition system of this specific bike that helped me gather the required data to make this determination:
On carbureted models, the ignition system consists of a signal generator, igniter with an 8-bit microprocessor (IC), two ignition
coils and two park plugs. During operation, the IC in the igniter
receives input from the signal generator, throttle position sensor,
and MAP sensor to determine the ignition timing for the operating
The IC sends a signal to the ignition coil, the primary winding turns
off and on, and a high voltage is induced in the secondary winding,
which fires the spark plug.