(1) It seems silly to bump the version number of a module just because of an edit to the MANIFEST. However, I can't just re-upload a module with the same version number. What is the proper way to deal with this situation (other than being more careful in the first place).

Simplest option is bump version number . Also happens to be most popular option. Say go from 0.001 to 0.00101.

You could try only changing the tarball name :) but meh

(2) If I upload a development version to CPAN (version number ending in "_\d+") will it still be tested by CPAN Testers? If so, clearly this would have avoided the current situation for me.

Yes it will be tested.