This is why I asked where you were in your life cycle.  

Putting in a hybrid change over system if it's not already in place is always a option but I wouldn't change anything unless it's at end of life cycle.

Capital and time are scare; so, ROI is important.This exercise could also be done later in the life cycle of your properties.  

What's probably least understood by the average lay person, allowing a package rooftop unit to operate in this fashion merely serves to shorten its life cycle in addition to costing more money to operate since the unit is consuming more gas and electricity in attempting to heat and cool the building on its own.

We may consider what specific value Jeff will add over the life cycle of the investment.

These are often sold at a much bigger discount than buildings built in the 1970's or even 1980's that are habitable but everything is at end of lifecycle. 

If you were using an IRR template for a 30 year Buy-and-Hold you'd show cost to rehab the property somewhere between years 12-15, and if you were going to really plan to hold at year 30 you'd show rehab/upgrade cost there as well, you'd also factor in a percentage of the cost of inflation for the rehabs, $5,000 for floors today most likely won't be $5,000 15 or 30 years from now.Maybe we can get the Bigger Pockets leadership to provide a good IRR template so investors can plan a complete deal throughout the property holding lifecycle.      

This is such a typical story of the landlord's career life cycle, sad really.

I know the boiler is at the end of its life cycle.

Last in terms of Capital Expenditures, as you stated the house is over 100 years old so these may need to be higher, the older the house is the more I would factor in for these, my house was built in 2010 and I had to shell out for a carpet because it's lifecycle had run it's course, I didn't budget for this properly initially and it came back to burn me.