In such a short time, I think I have encountered most nightmares of a remote landlord.  

Even as GC, we still encounter our subs started being very very good, then after 2-3 jobs they gotten comfortable, they started not showing or not having enough men power to do the job on time.

I've spoken with several hard money lenders (2-3) and it sounds like there are possible options, however the property (as is) would be considered commercial and therefore that complicates their process/qualifications.Has anyone encountered a situation like this? 

Yes you can stagger it to avoid "sticker shock" but you can justify the rent increase by improving the apartment (new paint, new flooring, new appliances, landscaping, etc).

You might also encounter issues from a tenant on privacy if you have a camera on the front door of the SFR. 

Has anyone encountered this with hard money guy trying to postpone closing date and contract stipulates I will be paying steep penalties if I dont close.Is this your experience, what can i do ?

It's certainly possible you could encounter a particular lender not willing to work with this but there is no hard and fast rule about having multiple owner occupant mortgages if you are abiding by the required occupancy period every time. 

Just wondering if others in the Syracuse area have encountered this problem and what they have been doing?

@Jason BoritzThe rudest staff we encountered (not rude to us but pretty much everyone around), was in LAX.

I would venture to say you  are going to encounter more problems as you start to fix things.