The agent said I shouldn’t do that, just keep the cash flow and say it’s my permanent residence anyways.

@Jermenta Gardner depending on your area a good driveway power wash can do wonders, for more permanent things nice or no carpet really helps, if the carpet is iffy, people don't fall in love with it.

My plan is to live in the 1/1 for a year or two until I find something more permanent for me.

d) I am currently waiting to hear back from the USDA Rural Development office, but I am worried they will require us to live there permanently, and I think it will be more of a back and forth property for us (5 months in the summer time).

It seems to be a permanent fix knock on wood.

However we do not want to permanently live in Syracuse.

You can certainly look into FHA 203(k) loans or construction-to-permanent financing. 

for the AC, one easy option is to put adjustable vents in the units and move the thermostat out of one of the units and make it set to some permanent temperature (e.g. 72 degrees) which you can control.

You can only separate out non-structural non-permanent elements of a residential rental. 

The reason I’m thinking of a 4plex is because I’d like to use an FHA construction to permanent loan with a 3.5% down payment.