I've just stumbled across this thread and I'm impressed! I've had FCR39's on my 950SM for a while and have been steadily working through all the issues you talk about... and the final issue is of course the choke. I wasn't brave enough to try to separate the parts of the carb body, but initially I also went down the route of trying to just add the appropriate parts. I came to the conclusion that it just wasn't going to happen easily enough and changed direction.
I'm 95% finished building an external choke circuit for each carb, controlled with the OE lever and cables. It's turned out a little bigger than it needs to be, but as a first prototype I'm pretty pleased. Best news is it works! I've yet to find the best setting for the air-jet (it's adjustable) and go small enough on the fuel jet (it's currently way too rich!), but I'm close. No pumping of the throttle, one-press starting from cold and a fast idle facility without twiddling with the idle-screws. Yay!
Just need a bit more quality-time in the workshop to get the jetting right and make a mounting bracket.
I'll try to get some pictures for you guys the next time I get to go home!!
In the meantime, please tell me where I can buy the 'velocity stacks'. I would really like to try those...