All perfect praise be to Allaah, the Lord of the Worlds. I testify that there is none worthy of worship except Allaah, and that Muhammad, sallallaahu ‘alayhi wa sallam, is His Slave and Messenger.
It appears from your question that what you had been doing is clear cheating and contravening the conditions of the company in deserving the fees from the advertisements; therefore, in order to be acquitted from sin from this money that was taken without right, you must do either of the following:
1- You have to seek the forgiveness of the owners of this company, and if they absolve you of their rights, then you are not required to do anything else.
2- If they do not absolve you, then you are obliged to give the money back to them, and if you do not know exactly its amount, then you should endeavor to estimate it according to what you predominantly think would acquit you from sin, but it is not sufficient that you give it in charity while you are able to give it back to its rightful owner.
As for your traffic in the site and your earnings from it, if it is lawful trade, then you deserve the profit. If you obtained the capital money in that manner as well as the house that was built from this money and with other money, then you are not obliged to get rid of it, rather you may dispose of it as you wish, by selling it, renting it or dwelling in it. This is because the money of the company which you had taken without right is a debt which you are personally liable to repay, but other matters are not related to this [i.e. the sin of taking that money is related to you and not to the money itself. For more benefit, please refer to Fatwa 130992.
Concerning what you mentioned in regard to contravening the law and using your contacts (to keep the government officials silent), then you are only required to seek the forgiveness of Allaah and this is the expiation for such actions. This has nothing to do with the lawfulness of the house and the permissibility of disposing of it as you please.
Allaah Knows best.