The home has appreciated significantly.I am having trouble refinancing because 1 condo owner owns 11% of the units in the association across multiple buildings, making it a non-conforming loan.  

Try to find one who holds their own paper and does their own underwriting rather than a large national/regional bank or mortgage broker that just wants to sell off a conforming note.Most hard money lenders will not loan on an owner occupied property, so that's a long shot.

In other words, did it used to be a legal non-conforming use?

Probably not conforming with all the local zoning etc.And they are probably keeping this under the radar to keep it financeable via a residential 30YF mortgage, which is a good thing for you.

., does not conform to today's standards, and needs to be repaired or conform to code by qualified licensed technicians.

My understanding is that the conforming standard is an allowance for up to 60 days. 

I just refinanced a duplex on a 30 year 4.75%. as long as the units are conforming and you have the value to get.

I'm telling yathis is not a easy taskyou have to have all your licensing in place first, plus it has to conform to ADA, fire marshal, and city requirementsyou will need a twenty four hour live in caretaker that is licensed plus a RN that is licensed with a certificate for home healthyou should probably look into the requirements in your area before even considering the scenarioI just went through this last year in AZ and I decided it was too much of a hassle even with my network at the hospitalenjoy

There is potential it could change in the future with the city plan, I could try to get a legal non-conforming letter from the city if its applicable and/or try to rezone it but what if I'm not approved?

Hopefully our FNMA/conforming loan gurus can chime in soon and lecture me about this, but I think you should be able to use all of your FNMA loans still and those other loans won't count against you using them.