Just checked the TPS and it was reading 10k with a closed throttle. Adjusted it to 5k now. Is that not ideal?
Yes, by the book but no by experience.
The stock timing takes account of poorer quality fuel worldwide, I reckon. The bike will take - and appreciate - a bit more advance on 95 octane fuel. So, bouncing between 5 - 10k is a good setting.
The partial choke call is a good one. Certainly worth confirming.
Likewise, the possibility of crap in the fuel system. If the FST and a fresh tank of fuel doesn't cure it, maybe drain the carb float bowls but be very careful tightening the drain screws as it's easy to overdo it and crack the float bowl. Those can't be bought separately ...
Another possible cause of a misfire could be plugs or plug leads. The caps take a firm press to push fully home. Also, consider unscrewing the plug leads, trimming 1cm off the end and refitting.
I'm sure you'll assume nothing, just because the dealer said he did a long pre-delivery service ...