I have sent them Jim's information and Jim has been in contact with them a few times as well as occasional emails from both of us. Maybe it would help to send them an email if you are interested. (And even if you aren't interested; may help us.)
For me, the problem was not having any support after the purchase and I am not going to hack ECU wiring and then find out there is a strange problem afterwards. PITA trying to troubleshoot electronics without any information or support. I would avoid them totally.
I had similar experiences when not using Yamalube on my 2001 previously. Rotella is also popular and works for many. After returning to Yamalube, my issues went away.
My father who was a Master Mechanic for most of his life once told me that if you change your battery every year or two, you will almost never have charging or starter issues. The starter doesn't get as hot and the alternator is not always having to compensate for a deficient battery. I have...
Almost very bike I have ever bought, I thought I would have it until I died. Ten+ bikes later, I still think the same but in reality, I have moved onto one after another. The parts issue has been this way forever; whether it be bikes, cars, planes or even a piece of heavy equipment...
Never had any issues with Shinkos at all. Been using them on my 2009 VMAX, FJR and 1st Gen VMax. Personally, I found the BattleAxe tires wore out very quickly. I would be checking headstock bearings, tire air pressure, wheels and your brakes.
I would venture to guess that you need spacers which should have come with the shocks as Progressives do. I had Ohlins for awhile but while looking cool, did not make my 2001 handle noticeably better than a new set of not expensive Progressives. Sold them. To run a wheel/tire combo that wide...
Try the Yamaha shop. Probably better quality and faster than waiting while you are in the middle of the project. Mine worked out fine but that filter mod is a PITA.