Miriam,
Using the 99 with a bent mainshaft should not cause further damage in most cases. I would, however, ask a few questions, before
Sewing with it. Do you feel any rubbing or binding? Does the large spoked handwheel rub on anything? If no to both of these questions, then I'd feel comfortable using the machine. The wobbly handwheel may drive you crazy, though. I had to straighten a bent shaft on a Singer 28 since I couldn't stand that wobbly handwheel.
Cathy