Sorry about that, it's a rather unfortunate, and common, mistake.
You only use them for adjusting the mixture. Synchronizing the carbs is done with the adjusted on the throttle shaft between the carbs.
The two adjustments are commonly done together, but neither one replaces the other.
Before you get too far along with your drilling and mangling, get out your Dremel tool and a large cut-off wheel. Cut a slot down the tower and cut a fresh slot in the top of the screw. You should then have a good "bite" on the screw and can remove it. Don't worry about the slot in the tower, it's all in an area where it doesn't matter.
Not the best shot, but if you look closely, you can see that both carbs have had slots cut to get the mixture screws out.
If the flat screens look fine enough to be the filters they are supposed to be, they should be no problem. If you are not comfortable with them, move your round ones over to the new seats. They just clip right off.
That is correct, they want you to drill the holes that are off-center in the bottom of the slide. Do yourself a favor before you drill.
Put a piece of wire or a smaller drill bit through the hole and notice that IT IS NOT DRILLED STRAIGHT, IT IS AT AN ANGLE.
.