Trouble getting good comps for duplex in my area

[Phillip Rosin]

I have two identical, adjacent duplexes and am wanting to do a cash out refinance on one of them once I'm done with rehab. I don't know that there's enough equity in the other at the moment to be worthwhile. I'm considering making that one my primary and staying a year, to get the best rates and a better LTV. In order to get a better idea of my budget, I hired an independent appraiser to give me a value after rehab. He ran into a few things and I'm wondering if anyone else has advice or experience with this.

Each unit is a 3/2, 1080 sqft. Located in Clearwater, FL.

Purchase price $249K. Appraised ARV $315K (By comps). WIth income approach, which he said likely won't be considered, $348K.

1. There are very few recent multifamily sales in the area and the ones that have sold have less than 3 bedrooms (typically they are 2/1). Further, I'm in an area with low crime but you head a mile away and it gets pretty rough. That is where a most of these comps are located. He said appraisers will only like at like properties withing a small radius and not use single family homes for comps, so I'm stuck with those. 

For comps with 2/1 units, he only added $3,000 adjustment per unit in comparison to my 3/2. I'm wondering if this is typical, or if that seems lower than an appraiser would normally add? The square footage was adjusted by $40/sqft between buildings. 

2. Since both duplexes I own are identical, and both were purchased for the same time and price, he's using one as the other's comp. This creates an issue because they both have been rehabbed and should be worth a lot more now, but the original sale price of the other is hurting the valuation. I'm wondering if there is anything I can do here, other than try to make my case by showing the work that was completed to justify a higher adjustment?

Any and all advice on getting the highest valuation and/or maybe some sort of creative financing will be greatly appreciated! Thank you.