I would recommend that you file the returns that is, the 1096 and 1099's Misc and dont worry about the penalties. There is no need to pay the penalties for late filing, and usually the IRS will assess this penalty on you. They will also provide you with an address to mail the payment.
So, in summary, I would not worry a great deal about this and just mail the returns as soon as possible. I have yet to see the IRS assess late filing penalties for delinquent 1096/1099-Misc filers. This does not mean that they will not assess you in your case, though, it seems unlikely to me that they would.