Thanks for the wiring diagram. That's is very similar to what I needed. I bought the manual from Yamahapubs online but the quality was so bad I could barely make out the wire colors 🤦🏼♂️ I'll see if I can get my money back, I've had good experiences with them in the past. Anyway, at this point I'm pretty sure that my ECU is bad.
The manual I bought is for a YFM35FGIX which seems to be another name for the YFM350FWAN. Wiring diagrams are exactly like the bike is. Only issue is the aforementioned quality problems...
Also, this is the manual I had seen on this site:
westomatic's post in 2008 YFM350FWAN IRS 4WD Wiring diagrams needed. was marked as the answer