Are the funds I received from the company as compensation for my usurped right and for the increase that was not paid to me lawful? Do I have to repay them in installments, and what about repaying what my colleague took? Is it permissible to repay them from the profits of my private business, which I established with some of these funds?

If the company has wronged you, and it becomes clear that you cannot obtain your rights except through stratagem, then there is no blame upon you, based on the permissibility of such action in the matter of overcoming injustice (mas'alat al-zafar).

As for what the partner took: if it was part of your right in exchange for his assistance, then there is no blame. But if it was an excess taken without a legitimate Shar'i justification, and you helped him take it, then you have sinned for cooperating in sin and aggression.

The responsibility for guaranteeing what was taken falls upon the one who directly took it: if you were the direct actor, then you must immediately return its equivalent to the company, and if you are unable, installment payments are permissible. If he was the direct actor, then you are not obliged to guarantee it, even if you assisted him, because the ruling is attributed to the direct actor. In both cases, you must repent.