It is unclear what your question is. Forgery, conversion and theft could all be crimes, so bringing this to the authorities could have negative consequences for your father. At a minimum I would check all your other accounts and verify that you don't have funds in common with him as he doesn't seem trustworthy. You should contact a local attorney to see about attempting to recover the funds if they were converted out of your account.
I would start with the bank by filing a claim there that your name was forged. The money represented by the forged checks will be returned to your account. Since the account is a joint account, your father would have access to the money again. You can't insulate your father from the consequences of an illegal act. Separate yourself from the joint account. Do not put your money there. Open a separate bank account. Good luck.
You should talk with an attorney about the tax consequences of re-titling the stock so that you each own one-half of it in your respective names. That would solve the check cashing problem.