So I posted earlier that I dropped my bike off on the 22nd of July and I wrote that I needed the full harness recall. I called again today and asked for an ETA, the parts dept. is closed on Mondays so they couldn't provide any information other than they were waiting on parts.
I decided to call Yamaha directly to inquire about what was taking so long and ended up talking to a guy who called the dealer on my behalf. The Yamaha rep told me that the dealer that they had ordered the quick fix harness, not the full harness and was waiting on an ECU to fix some altitude issue which is unrelated and separate from the grounding issue. Yamaha rep basically said that if the harness wasn't melted that the quick fix was all I needed and I could be back on the road and could do the ECU fix whenever they got the part in.
I'm a bit confused because the dealer doesn't appear to be providing me all the information but it would sound like I should have had my bike back several days ago, I'm not going to be happy if this is the case. I should know more tomorrow.