Security deposit can be used to cure this. 

Tierra,General rule is 70% of As Repaired Value  (ARV) minus cost to cure defects  (in your case 30k).

What I would like to do would be to acquire the land and build the home and then pro cure a USDA loan for the property and home.

In that 3 days, he did pay rent, but did not cure or "undo" the house modifications.I would like to file the eviction based on him not curing the house modifications.From my perspective a breech of the lease is a breech of the lease.  

If so, do they translate to rental increases or is it related to curing deferred maintenance?

You can't cure all ills.

Do those same concerns apply if you are buying a tax certificate over the counter from ADOR a year or two after the tax sale, or is the "void" nature of the sale essentially cured by then?

If you’re painting, there are some really great cabinet paints out there now that cure super hard and are very durable.

You state will have information about how you can post a "cure-or-quit" notice regarding non-payment of rent (ie if he doesn't pay rent on the 1st, like the lease says, you can give him an official notice to Pay the rent or you will proceed with an eviction).  

In the event they do, you can Deed the property back to your sister for a time, to cure the default.