The primary bushing kit is another mod that I put into the "only if another base plate cannot be found or it's rare carb" category. For that much money, a guy could prolly find two or three cores that need nothing done to the primary throttle bores. Now, if cost isn't a primary consideration, for sure go ahead and do it. Hell, RPD should have installed bushings from the get-go, IMHO. Secondary shaft wear hasn't been an issue w/any of the carbs I've seen.
Whether or not the wear is going to cause idle problems (at speeds above an idle, the shaft play is not a consideration) depends on just how significant the wear actually is. This can be judged by if the primary blade on the throttle linkage (left) side of the carb can touch the throttle bore, and/or by how well the carb will hold a steady idle, w/o it 'hunting' or being erratic.
A lot depends on how the return spring was set up. If the spring pulled rearward (same direction that the throttle cable pulls) from the lower part of the throttle arm, wear can occur within the life of the engine it was installed on because both the throttle linkage AND the spring is working together to cause twice the wear. But if the return spring was hooked to the upper throttle arm and was attached to a bracket forward of the carb, this will act to offset each other and the wear will be less.
As far as milling the main body, the boosters are above the plane of the gasket surface and they are not removable. So milling the body would be a machine shop-type op, as far as I'm concerned- I cannot envision doing this on a belt sander w/any real hope of success. In any event, it's going to be the airhorn that's warped in the majority of cases, anyway.