I wanted to seek your advice because on one hand, I have tenants that need to be taken care of with proper living conditions and on the other hand the company I've hired to do that is negligent and can't be trusted to do the right thing.I want to fire this company but should i wait until repairs are complete? 

I have language in the lease that says repairs required due to tenant misuse or negligence are the responsibility of the tenant.

Once the LLC is the borrower, not you personally, it frees up your eligibility to obtain more properties using Conventional financing again.The cost of each Conventional loan is negligible compared to the cost of commercial/portfolio financing, which likely also will have a higher interest rate.There is a LOT of strategy and future planning that you should be doing, and that's why it's critical to have a great team looking out for your best interests and not just on the current transaction. 

This is an amount of money that cannot be ignored and if there are real issues of negligence, they need to be called out.  

The other repairs should be done as close to the inspection date as possible just in case your tenant’s negligence undoes your good work before the inspection. 

You would be the trustee.Keep in mind that a lawsuit would need to prove that you were negligent in some way and it caused harm to someone before you would have to pay any money.

What do you do if you have a tenant who is just messy, versus a tenant who might be causing damage to the property due to negligence (e.g. letting food rot, attracting pests)?

You'd also likely be entitled to the buyer paying other damages as a result of his negligence and attorney fees.

They both can be held liable and were both negligent on some level.

So you just went from negligence to willful attempts to deliberately evade taxes -- have you looked at the definition of tax fraud recently?