It seems that despite the fact that you have formed a C Corporation, you handled all your activity as a Sole-Proprietorship. Whilst this may have been bad from a legal standpoint of view, from a tax point of view, you may have come out ahead for the tax year. The reason is I am almost certain that you did not take a salary from the C corporation, because all the monies collected from the Salon were deposited in the Sole-Proprietorship bank account. Thus, you would be required to a file a limited activity C corporation tax return, but you would have to file a Schedule C reporting all your salon activity. In other words, the double taxation issue may not be an issue for you.
I would immediately hire a CPA and make sure that the above is true and that you now operate your business properly as a Corporation and it is imperative that you have the CPA convert your corporation to an S Corporation. Thus, you would avoid the double taxation scenario.
Here are the answers to your specific questions.
1. Am I too late to make election to S-Corporation?
Generally speaking yes for the past year that is, but you must apply for an S corporation within 2 1/2 months of the new tax year 2009.
2. Can I still file my return as Sole-Proprietorship or I have to file 1120 Corporation?
You be required to file a C Corporation tax return as well as filing a Schedule C as a Sole-Proprietorship, with your net income subject to the 15.3% S/E tax.
3. I have no employee, do i still require to file form940 and 944 as it said when I recieve my EIN?
No, you are not required to file these forms.
4. With a c-corporation, am I still required to file individual 1040 return correct? double taxation?
Yes, you should file a 1040 tax return, and the C corporations are generally subject to double taxation, but only on net profits (see my comments above).