Hello again and thank you for your response. This issue really must be dealt with by a local forensic accountant who has payroll expertise and also a local employment law attorney. It sounds like it is beyond you handling this on your own at this time and since DOJ is involved, you really need a local attorney to assist you with that issue.
What I can say is that as far as the current employees' wages go you must pay them in the same pay period that they are normally paid in for the hours that you and they can agree that they worked. As long as you make a good faith effort to pay them properly, the DOL will not fine you for underpaying them and you would not normally be liable for any penalty for paying them less than they were due. But, it is important that you sit down with them if you don't have their schedules and can't figure out the time clock (or it wasn't used) and ask them what their hours were for the pay period. It is much better to overpay, than to underpay them and if your records are not currently clear in the hours they worked, you have to get them paid some way. Then, as mentioned, you need a professional payroll person to help you get back on track and figure out what records you can find for down the road.
I can't really address the bartender tip issue other than the same way, if they were paid their tips in cash, then if you need that information and don't have it, you have to ask them. It is better than nothing, which is apparently what you have now. If their money has not been paid to them, and it has disappeared, then that might necessitate a criminal complaint against the manager if you think they took the money.
As for the manager, if you can prove that you had already changed him to an hourly employee and that you had paid him his wages (including overtime) for hours he actually worked, then you have complied with the law. But again, if you have the DOJ contacting you then you need a local employment law attorney involved along with the forensic accountant. You wouldn't have any sort of action against him for harassment since it is within his rights to pursue his wages, etc. You could though, if you hire an attorney, have your attorney send him a letter that lets him know that he is to contact your attorney now and not you.
But again, you have to keep paying your employers for all of the hours that you and they can agree that they worked. If you don't pay them when their payday is due, you will face some serious issues with the DOL and could be facing penalties.
Please feel free to ask for clarification if needed.