I have never operated a franchise, I did look into it.

If you do not get it at your price you walk.Always remember business does not operate successfully on emotions unless a sellers emotions are a weakness you can exploit.

In a training program I did I was taught to estimate costs at 50% of gross income when analyzing the financials, but after looking through dozens of marketing packages I have only found 3 where reported expenses even approach 40% and most are around 30% or closer to 20% of the operating income.

Can it be argued after having transferred tittle to an LLC all finances going foward weren't commingled and was operated entirely as a seperate entity.

LLC will increase your costs to operate as well as complicate your taxes and mortgage/financing.There is actually very little need for a LLC beyond physiological protection and for that reason you are probably better off not transferring at this point in time.

Other investors and lenders like to see overall performance first (overall gross and net profit, operating expense, annual return in percentage etc).

On the HUD website it says only that: At least 80 percent of the units must have at least one occupant who is 55 years of age or older; andThe facility or community must publish and adhere to policies and procedures that demonstrate the intent to operate as "55 or older" housing; andThe facility or community must comply with HUD's regulatory requirements for age verification of residentsThis all seems a bit too easy to me, but can't really find step-by-step directions anywhere to do this.

Money is made when you buy , not when you sell  Yeah I mean I guess this is true, but I suppose my confusion is how a property that hits every benchmark imaginable as laid out by members of this forum (1.1% rent of all in cost, <50% operating expense, 28% cash on cash return) could turn into such a burden on a simple refi?

Unfortunately there is no individual or specific governing body in regards to property management in NY State so there are a lot of illegal companies pretending to be property managers and there are serious consequences for operating as a property manager without being properly licensed in NY.

Besides your operating agreement needs this roles' breakdown anyway.