Thanks for the tips guys.
So I pulled the bike apart today and found some tell tale signs of what my research has told me is a failed balance shaft seal. The front carb intake had a good bit of oil on it with some pooling beneath the carb. So, I made a two hour drive to the closest KTM dealership, picked up the new seal, and installed it tonight.
I capped the crankcase breather hose fitting on top of the air box and placed a seperate filter on the hose itself in order to prevent any further oil intrusion into the airbox.
Additionally, the BMC air filter looked pretty dirty so I cleaned it (currently drying).
I also noticed the PO put a filter on the carb breather hose (the bike has 1 x capped tube on each carb, with the remaining 2 x tubes joining to a T-fitting. From the T-fitting it goes to a small filter). Anyways, that filter was insanely dirty, smashed up, and straight nasty so I replaced that.
Hopefully, once the filter dries and I get the bike back together, these changes will fix the problems.