1) If you are comfortable with setting up your drill press and can successfully drill BOTH sides of the flange in one pass, then you ar professional enough to do this.
2) I have not done this myself, but I believe the specs for the diameter of the HOLE and the size of the throttle SHAFT have been posted....maybe by Derek Eddlestone?
3) The corrosiveness of modern carb cleaners is nothing like the old days, but that stuff went into the water and caused all kinds of hell downstream so the EPA made them reformulate it and...it sucks. Soak it in that stuff or some other home remedies I hear you can find under the kitchen sink...and then LIGHTLY go over it with Soda Blast (or the wife's Baking Soda) which will clean the rest of it up nicely without giving it a glistening shine like polished aluminum...which they never had from the factory. After that a simple rinse in WATER will dissolve any remaining soda and wash it away...you then need to dry it out in a WARM oven when she is at the beauty salon...The flange should be "parked" with an Iron Oxide finish to give it a greyish dull finish before you bush it...(Black paint or other parkerization chemicals will give different, i.e., WRONG factory finishes to it otherwise).
Post some pics Jim or check jeepdraw to see if your carb is a 100% 539S or if it is another victim of post-war rebuilds and is a "carburetor salad" mixture of Carter parts or not. If you plan on doing a QUALITY restoration, you probably want to obtain the components for a 539 and restore them for this project.
GPW 17963 4/24/42 Chester, PA. USA 20113232 (est.)
GPW 85976 12/9/42 Louisville, KY. USA unknown
GPW 108552 4/21/43 Louisville, KY. USA 20371278
Bantam T3 4582 10/29/42 USA 0173499 (est.)