Hi Dave,
Do you want to remove the index completely from the output? If so, uncheck indexes here
I could add an option to show NUMBER(11,0) instead of NUMBER(11) if that will make your life easier, but that won't help you unless you're willing to wait for the next Toad version, or try the beta.
Regarding the rest of your message, I'm not sure what, if anything, I can offer. But if formatting is a problem, you could maybe run both Oracle's DDL and Toad's through Toad's formatter to get you closer.
-John