According to the Jenks Tuning Guide, an 865 Thrux with open exhausts and airbox removed should be 140 main jets, 40 pilot jets, 1 shim on each needle, 2.5 turns out on the idle mixture screws. Check here:
Jenks Tuning Guide
You can download and print the whole thing as pdf by clicking on the link.
On a warm day, I pull my choke out, start the bike, let it warm for about 30 seconds, push the choke in to half choke, and take off within a minute or two. Within one to two miles, I push the choke in to off. It doesn't have to be fully warmed up to reduce the choke; you just want it to be able to take some throttle so it doesn't stumble. For the first few minutes, I will be careful when taking off from a stop, feathering the clutch and giving it some gas so it doesn't stumble and die. On a really hot day, I will usually start with only half choke. Every bike is different, but I would be hesitant to let the bike idle long enough to build up to 2000 rpm when the engine is cold.
When is it fully warmed up? Different ideas on that. I usually take it easy for the first 10-20 minutes of riding, but that doesn't mean that's how long you need to leave the choke on.
You're right about not wanting the bike to sit for long at idle.