Well, if you have w-2 for $12000 then you will be able to get some tax refunds. If you add that 40K income as cash you will end up paying 2-3 k on the top of your refund plus interest if the tax due is over $1000.

Best bet is file single as w-2's income. Past is past and prepare for future. Now on you can pay taxes for your cash income , make sure you pay federal tax and state tax on it.  There are some limitation while you file tax with an ITIN holder.