The roof was in very bad condition (and the seller didn't want to fix anything).

Current need is drywall repair and paint, tuck pointing, subfloors, floor refinisher, tile, kitchen and bath, roof/gutter.

It took the roofs off and filled them with water. 

The agent confirmed to me that regardless what my inspection turns up, even if the roof is falling in and the foundation is crumbling, if I cancel the deal for any reason, I still lose the "option" money paid up front.

Roof was done as well as HVAC plumbing and electric.

Depending upon the roof truss's sometimes it's not real expensive to run duct work into the garage (but in this case it sounds like the existing hvac won't make that work). 

What would you look for the most other than HVAC, plumbing, roof.

In order to determine if $5k capex is a good number, you should have an understanding of the remaining life in the roofs, and how much replacement will cost, whether windows are needed during the time you'll own the buildings, HVAC life expectancy and replacement costs, etc.  

Then - plan for capx like roofs, windows, driveways, siding, HVAC systems.  

As you've implied, how the attorney drafts your contracts is a key aspect to the strength of this deal.