Your property sounds to be more unique, therefor likely making it challenging to find acceptable comps. if the property is common for the area, it's likely this could be a non-issue with the right lender. 

We have had some issues with getting insurance for the Florida properties in the LLC and also related issue with the Mortgage (which is in our name).When our lawyer requested EINs for the LLCs we were informed by the IRS that we need to file a 1065 for each of the LLCs.Our structure is that the LLCs are owned by the two Trusts (50%) in each of our names.

Have them pay for it and tell them you will reimburse them if there is a structural issue to the exterior sewer line. 

Credit score shouldn't be an issue.

This may be a case where you are trying to force the issue by wanting to complete a flip transaction where your market is telling you its not the right time.

However, if you're using a discount company that's allowing you as the owner to set the rent price, approve or deny apps, etc. then your issue could be one of many things. 

However, for the seller to net the agreed price, the price has to go up in which case you can run into the issue of the property not appraising.I think the fundamental issue is this requires a more sophisticated buyer and seller (especially to have a graduated commission scheme which is common in commercial). 

Now though, it’s a real issue because it’s affecting my rental income.

Although we didn’t have a move in move out list at the start of the lease, we have all the communication from the beginning to prove that they reported every issue and we took care of it.

This means expect tax increases, expect HOI increases, expect tenant issues, PM issues, capex issues, everything in between.