The flange is hardened, and a standard bit barely makes a dent. Special drills and taps are available, but would cost as much as a new gearbox.
There aren't any machine shops nearby, and I haven't ever seen a used 2nd gen gearbox offered on ebay, so I'll just bite the bullet and buy a new one and consider this another hard-learned lesson: When in doubt, look it up.
Thanks for your suggestions.