Should it send off alarm bells to a potential investor not to buy a property if the seller claims that he/she does not know the age of the roof, does not know if the roof has ever been replaced, does not disclose the nature of a minor repair to the roof, or what the original material that was used for the water pipes, although some of the pipes were replaced with copper, and if the seller claims that he/she is not sure of the age of the gas water heater, but claims that it was replaced 8 years ago with a major rehab?

A lot of what I'm seeing is 2 unit but has enough square footage for 3 units if the unfinished basement/potential garden unit is legal (assuming this would cost a pretty penny to make legal if not).

There's no right or wrong answer per se but also try not to be "penny wise and pound foolish".  

If there is any gray colored plastic pipe with crimped copper bands around the fittings, REMOVE IT!  

If the house has no hvac at all ( meaning new equipment,  registers, ducts, copper, drains, etc. all need to be installed) then $4500 sounds like a good to great estimate.

(Ex: bare wood on house $15 per day, unsecured building $150 per day, refrigerator outside not on its back with doors off 200-250 per day because tipping danger with kids playing around could get stuck inside)However with administrative liens, most can be negotiated for pennies less admin costs as long property has been brought into compliance.  

The bank will just write it off and short the next stock dividend by a penny or two.

Like @Ryan Pemberton said.IMHO - you should NOT be managing your properties and it's worth every penny to pay a great property manager to do what they do best!

We do not need a commercial building so we are in the works to have it remodeled as a residence, and that will probably cost a penny or two. 

If your life were depending on it, I bet you nickel for penny that you would have time for it.In my case, when I say I'm busy, it means I'm having too much fun.