I want to refurbish the entire house, including a complete kitchen and baths renovation, add an addition on the east side, new roof and siding, new flooring everywhere, paint inside and out"Then ask the GC to go over and put this into a more formal document.

Any person who can achieve property ownership, and then help others have a roof over their heads is a person worth high praise. 

The worst experience we've had was with a flat roofer (very common roof type in Chicago) we finally wrapped up, after waiting almost two years for them to finish/fix something. 

First you need to learn to separate the following:Maintenance: usually things related to wear & tear or tenant damage.Repairs: usually broken items like doors & windows, caused by tenant or nature.Capital Improvements: usually expensive things that wear out: hot water tanks, furnaces, roofs, etc.The seller is correct that Repairs & Capital Improvement items should not be a factor for awhile (ALWAYS get your own inspection to confirm).

Labor/material are going to be different and need to factor that in4) new roof, new HVAC, new water heater, ac panel, replacing plumbing to PVCThese are very variable, if you are getting this from a licensed guy to do it and unlicensed.. is it a big shop or a local shop doing it, is the GC doing it they will put some money on the top so it will be more money5) framing (creating new bedrooms or baths)I would get all these quoted from a good couple of licensed guys and unlicensed to know your numbers to cents

To avoid the risk management/insurance that comes with tenants' wood fire use:I'm thinking to seal the chimney cap on roof and run a cord putting an electric Infrared heater fireplace in there, so they can still open the glass and get heat and watch TV over the mantle, but can't burn anything or have any flame.

Prices are through the roof in this current market with low inventory and single and multi family properties just don't pencil out.

Metal trusses and roof.  

The roof and gutters are only a year and a half old.

Inspections--house, termite, possibly separate roof and structural8.