You probably won't be able to remove the broken screw in the throttle shaft, it sounds like the first time I removed them on my '81 R65, even with filing the peened end down, the screw would not come out .
I drilled out the remaining screw and got a new throttle shaft, there is very little thread on the throttle shaft that the screw threads into .
On the carb top you may have to drill out the screw as well, you can drill off the screw head to get the top off, then decide on where to go from there, I would use caution in using an 'easy-out ', if the screw is seized in there you may break off the easy-out in the process and compound your problems .