Initially, they didnt want to use agents but now they have pulled in an agent that is a friend of theirs and said this agent will do the paperwork.

If/when their hours go back down or things change again, they just have to submit new paperwork and the amount will change again.Also, did you submit a rent increase with the renewal?

How would this be set up with paperwork.

Because of this smaller budget, the paperwork is less involved, the construction draws are 50% up front and 50% at completion, and the work does not require a hud consultant.

The three items you mention are pricey, but not that hard to pay someone to do.Have your dad talk to a realtor-not sign any paperwork, to get an idea of market value as is and with the new roof, hot water tank, HVAC, a fresh coat of paint, maybe new kitchen countertops (and hardware), but leaving the bones as is. 

Now, when we brought these strategies up to our CPA, he told us it would be a lot of paperwork, and tried to talk us out of it (because he was being lazy)... so we found someone new to work with.

Often it comes down to getting the heirs organized and get them to sign the necessary paperwork.

After some negotiating and paperwork, the house is all yours!

You also have to file special paperwork with the IRS every year that the company you hire will do. 

Being an agent means helping you navigate through paper work, legal docs, and helping you stay on track with closing.However with that being said, make sure you follow the contractual deadlines, contact title and get things ready.