I'll just toss this out, and you can do with it what you want, but from what I've read and experienced with my bike, the stock carb tends to be lean in the primary circuit. There are plenty of people who still use the 35 and are fine, but I notice quite a few have stepped to the 37.5 or even 40. You might want to trade the 35 pilot out for a 37.5, and see what happens. My cold starts are by the book now regarding how long the enricher needs to be out.
I think the factory purposefully detuned these bikes in a big way, so they'd skip past the EPA.

You may know this, there is a cross reference chart on the Tech Articles page so that you can do a size comparison between the Mikuni and DJ jets.
If you move the clip down to the 3rd, or the 4th, you will probably see a change of sorts. I had an aftermarket needle in my carb when I tore it down after I bought the bike used(I was expecting to see a stock one groove needle), and it had the clip in the 3rd with a 165. The bike showed the classic lean symptoms with the WOT test. At 95,it seemed to be out of steam, and it would surge when the throttle was held steady. That is gone now. The bike pulls strong now. 45 to 80 or so in 4th, almost makes me think some velcro on the seat, would be a good idea.