...
Runs great and shifts a lot better

Some have said it’s the fresh oil not the filter. The oil had 3000 miles on it. I am by no way advocating for the 9k mile oil change
but would 3000 miles be enough to make it shift poorly?
Sure, if the oil wasn't up to scratch for whatever reason, it could do that within 100 miles! Any chance the oil was the wrong grade; not JASO or Motorcycle rated; or had been contaminated by something?? No-one that you're aware of had ever added 'friction modifiers' or any 'oil life extenders' to the Spyder's oil, had they?? Not even a few oil changes back??
There was one fella here in South Oz having all sorts of clutch and gear shift issues (not that he ever really pushed it much!

) and we'd tried
EVERYTHING we could think of to help, even changed the oil and filters a couple of times, and we'd get it to (apparently) work OK up here in the Hills when it was test ridden afterwards. But then the clutch slipping and gear change issues would come back just as soon as he got it home and started riding it around the city again -
every bloody time!! 
I even went down there & test rode it just to make sure it wasn't simply due to him being too hesitant & slow on the changes - he really didn't ever go much over 35 mph (not even on the freeway!) and it was definitely having gear change issues, plus, once things warmed up, some clutch slippage.
Then finally, it all became clear when I thought to ask the ^ question at the end of my first para... to which he replied, "
Sure, I've always added 'some proprietary brand of friction modifying stuff' to the oil in all of my cars, and they've lasted hundreds of thousands of miles without a problem. I want my Spyder to last that long too, so whenever I get the Spyder home after having had an oil change done, I suck out a litre of oil and top it up with friction modifier. Why do you ask?"...
Let's just say that the discussion that followed was very enlightening to him; he no longer adds any 'friction modifiers or oil life extenders' to his Spyder Oil; he does ride his Spyder a little harder; and he hasn't had any clutch slipping or gear changing issues ever since we finished
the third '
full flush oil & filter change'!
So, is there
any chance that someone might've used the wrong oil &/or added any additives to the correct oil in your Spyder??

If so, that certainly might have been contributing to your issues, and an oil change (or two, maybe even more) may have
finally got all the nasty contaminants/friction modifiers/oil life extenders out, hopefully without damaging too much
Just a thought, tho!?!
