I am looking to possibly rebuild the second home on the lot but don't want that to impede my non-conforming use of the property. 

Hi Ryan,Just off the top of my head, here are some of my thoughts.Look carefully at the zoning and see if there are other possible uses allowed for it's zoning type (and see if the zoning conforms currently).Such as Med/Dental (prob require an elevator), or whatever besides just office space (is the living space unit non-conforming--is it Grandfathered in, what triggers the end of the Grandfather, has that happened, will a sale make that happen (???)

To help veterans and active duty (and of course, eligible Guard & Reserve) buy a home, the VA through the VA home loan program will guarantee 25% of the purchase price up to a certain amount (usually known as the Conforming Loan Limit), enabling us to buy a home with a 0% down payment and no PMI.  

Another idea is the non-conforming duplex.

With all of these older properties, if they go vacant long enough or if they burn down or are destroyed then you lose your grandfathered zoning and would have to conform the modern zoning status.

Conventional fannie/freddie loans will be resold by the lender and need to conform to strict rules.

Though I have seen times where that not the case.Both FHA and Conforming have loan programs that can also lend you the money  for repairs.

Currently the Fed has a policy of buying unlimited mortgage backed securities, meaning there is no risk for a lender to originate loans that conform to Fannie Mae or Freddie Mac underwriting standards. 

They will compare the various contractor bids and make them conform to the consultants prices and time frames, unless the contractor can justify their differences.

@Andy Bhuchar This is more common than not, especially if it is a conforming loan transaction.