Ok so here is most likely the final update. In the original post I had mentioned that I was ordering the Yamaha computer diagnostic tool. Well that was on national back order and I would not have gotten that for a couple months. So I ordered the OBD/GST wire kit I had also mentioned in the original post. I got that today and it worked, however I still have a check light being kicked and I'll get into that at the end of the post.
So the OB/GST wire kit will indeed work with ANY OBD II scanner and clear the code properly. This is what I got with the wire kit, and OBD II connection with the R6 connector and a three way connector which I believe is for the dirt bikes, but I am not sure. Then I got another three pronged wire with a positive and negative and some other lead. I'm also not sure what these are for. This kit costs about $85 from the website I mentioned, perhaps you can find one cheaper. The part number is listed in the service manual.
Then you connect the OBD II into ANY motor vehicle scanner. Such as this one that I purchased for about $60 today at my local store. It reads and clears codes.
So then you connect it up into the square port on the bike, just to the left of the battery near the ECU
Once the scanner loads all the way in, some devices will want you to select a vehicle. Just select one, it doesn't matter. OBD codes kick out the same way. I selected Suzuki, Toyota and Honda and it spit out all the same code - P0746 which in the service manual, translates having to do with EXUP valve that I removed. So it will read the code and then I clear it. The light goes away and all is OK. Now for some people this will be it, they unplug it and go on their merry way.
For me, I purchased a Dyno Jet EXUP removal module from Cycle Gear. Got it, installed it and it threw the light. Which brought me here. I asked for them to send me another one, got that one installed it, CLEARED the light and about 10 mins later it sends the light again. SO I called Dyno Jet and they provide no support for it and it even says on the paper work that gets sent from Cycle Gear that it works on the 2006-2010 model. Now you and I know that from 2008-2016 the bike hasn't changed much, but PERHAPS 2017 did which some of their electronic components with their exhaust especially because the EXUP Motor is actually under the fuel tank now and not behind the rear spring. So I called my local shop and spoke with a tech there and he said that the only people that offer support for the EXUP eliminator is Graves Motorsports. Yamaha also lists them on their manufacturer website and offers it as a OEM type of after market part. Also via their website, they say specifically it will turn off the engine light with regards to the exhaust issue. Now for face value, they look exactly the same, pictures on websites I can't tell a difference. But maybe there is something, so I ordered that and RMA'd the Dyno Jet EXUP and am waiting for the Graves part. Just FYI, the bike runs perfectly fine, it is NOT in a limp home mode and it DOES allow me to switch TCS modes and Ride modes without issue.
However, that is my issue and if that doesn't work then I may have to flash the ECU over the winter time when I am not riding. I may end up doing it anyway, so if anyone has anyone reputable for flashing the ECU, let me know.
I also have attached some final pictures of the bike and this is what I have done to it so far; M4 Y-Pipe (cut the cat off like on the older models), Akrapovic new 2017 GP Slip on for this model year (No different from the others, however it is the WSBK look), Power Commander with a custom map (available if anyone would like it, PM me), the Yamaha Up Quickshifter, Graves frame sliders, Yamaha engine cover kit, rear seat delete (IMU may be coming), and mirror block offs.
So I hope this helps people in the future and if you have any questions, I could try and answer them.
For the service manuals visit Yamahapubs. They have the e-book for like 14$. I couldn't manage to rip it off at all.