As an appraiser, I have a few tips for you that may help. Pull the comps you feel are the Most Similar to your property. GLA and condition are pry two of the most crucial items. Now every appraiser analyzes the market data different and you can tell by reading your entire report. A lot of people just look at the number and not the information that is in the report.
When you are searching for comps try not to search with a specific price range, it narrows your view and is like putting blinders on. Now once you have at a minimum of 3 similar comps take that information to excel and make the same adjustments that the appraiser made and that will come up with a similar adjusted sales price the appraiser would if they use your provided comps. I have had it many times where they want me to consider additional comps and the comps hurt the value even more.
Now the comp that you state is a short sale that needed work, is it marked short sale in the report? If not the appraisers' information could be wrong. You would be surprised at how many Realtors put miss leading marketing information in the MLS. Realtors jobs are to sell homes and to sell homes you need to get people in the door. So often they put a lot of fluff in the MLS to try and get more people to come to take a look at the home.
One appraisal I was working on I was having a hard time proving sales price. Call up the realtor who had sold many of the comps I was using in the area and asked what comps he used. He told me and started telling me how this one comp, that I thought was the most similar based on the data I had including his listing information, was junk and needed so much work and not as nice as the subject. I told him that is not what you marketed this home as. You said its move in ready, well maintained and that it is so clean.
So look at all the data, read the report and if you have conflicting information provide that back to the appraiser.
I will be posting some post here in the future on how to pull the best comps and created a more accurate CMA and best practices for Realtors to help keep appraisals from coming in "low".