I'm would think your rental is current and in good standing.Properties with the same bath and bed and land.An appraisal is just an opnion of value so if you can show a different picture and nicely give the second appraiser these comps that you found you'll likely get a higher value.Also remember that most value is improved with additional SQ footage, new bathrooms, new kitchen. 

Most likely the appraiser will use the total square footage, and number of bedrooms and baths for comps.

I bought a day pass to get addresses and square footages of all 2/1s within a half mile radius of me and filled out a matrix similar to what you were describing.

Also full basements because the square footage doesn't count toward FAR or max lot coverage.

I would not worry about the painting, the appraiser is going to look at the value of the home based on other homes of similar square footage in the market.

Can you use a 4bdrm comp against a 3 bdrm home if the sq footage and age are the same and do a 3k adjustment for the bedroom difference?

Our retail space, although on a high traffic street that I thought was great, has just a bit too much square footage for most businesses to take on, so it sits vacant-a lot. 

I have no problem with an appreciation play, but not when you have to add square footage & spend an additional 100k to make a profit.

I still don't know if your project qualifies for a 221 loan since you haven't mentioned how much square footage the commercial space occupies compared to the total square footage.

But, if something happens to THEM or their stuff, I would share footage with them and authorities for their benefit.