I don't believe that your employer ever paid the withholding to the IRS/Social Security when he paid you with his personal checks. That's why he gave you the personal checks, because he didn't have enough money to pay the employment taxes. This means that your Social Security Account and your federal and state tax agencies have no record of these wages. This means that your W-2 is incorrect. There shouldn't be a 1099 for you, because you were an employee!

 

If you didn’t get your corrected W-2 from your employer by February 14th, and you contacted your employer and still haven't gotten it you should contact the IRS to tell them your employer didn't send it. You may call the IRS toll free at 800-829-1040.

• The IRS will send your employer a letter requesting that they furnish you a corrected Form W-2 within ten days. The letter advises your employer of their responsibilities to provide a correct Form W-2 and of the penalties for failure to do so.
• The IRS will send you a letter with instructions and Form 4852 (.pdf), Substitute for Form W-2, Wage and Tax Statement, or Form 1099-R, Distributions from Pensions, Annuities, Retirement or Profit-Sharing Plans, IRAs, Insurance Contracts, etc. You can use the Form 4852 in the event that your employer does not provide you with Form W-2 in time to file your tax return. 

You can prepare a return with Form 4852 in TurboTax.

• Visit the W-2 area of TurboTax and choose "Work on my W-2 now".
• Enter the Employer ID Number (EIN) if you know it. Leave it blank if you don’t.
• Enter all the info that should be on your W-2 if you actually received it. Use your pay stubs to estimate what your total income was from this employer and what your total taxes paid were (include federal, state, and local taxes). Essentially, you’re trying to re-create your W-2 based on the best information you have available on hand (pay stubs, bank statements, etc.).
• Write out an explanation of how you figured out your wages and taxes paid.
• Describe the steps you took when you tried to get your W-2 from your employer, like who you contacted and the date, etc…
• After you’re done estimating what your W-2 should look like, click past the W-2 area and select the checkbox for “I did not receive a W-2 from my employer and need to complete a substitute form”.

See this information from the IRS.

 

I would check with your employer to see if he did pay SS and Medicare taxes on these wages. If he did then you should get a corrected W-2. If not, then follow the advice others have posted.

I am in a very similar situation with my ex-employer except he did not give me a W-2 at all. But I am certain that he did not pay any taxes on his employees wages. I tried following your instructions below except there is no place that I could find while filling out the W2 information for notes. And on the following page where it has the list to check the boxes, there is not an option for did not receive W-2.

When you are completing the Form 8919, you do not want to use Code H if your employer has not provided a 1099-MISC to you.  You have not way of knowing if he  will- so you are better using the G code (after you complete an SS-8).  Yes, you can use the estimated amount if you are not 100% sure but be sure to keep copies of the bank records you used to determine the amount. 

 

After the IRS makes a determination, they will contact the employer for the employer's share of the FICA taxes.

 

If you did not receive a W2 at all, you must also complete the Form 4852 (substitute for W2) and enter as much information as you have. 

 

If you have more questions, please let us know.