You need to put your firm foot down with this guy.

Once you receive an approved building permit, and at the last minute decide you want to extend the porch a foot out, or add a covered deck, what would the typical process to do so be?

My biggest question is if there should be some sort of fee for essentially doing the foot work, finding the property and going through all the steps given the down payment is being paid back.

Four comparable homes within a 5-block radius have sold for an average price per square foot (I was a local appraiser here for 6 years) that would indicate a sales price between $87,755 and $89,863.

there are so many 2 family homes with all kinds of configurations there. the best you will be able to do is try and match the rest of the house, square foot, number of baths etc. you may be able to get away with a 6 bedroom house as a comp, 3 and 3. i know i am having the same trouble with a house i own in PA, its under contract but when they came back there was no exact comps to mine, we are in the process of fighting what the appraiser came up with right now, they came up with $38,000 under my list, but i know i priced it right based on price per square foot and whats in it, 2 family with 3 and and 1 bath each. try averaging what a 2 family sells for per square foot, that should give you an idea. then sell it to me for 100,000 less - just kidding, but you can let me know if you do decide to sell, I'm in the town next door.

I'm gonna move to Colorado if a 5000 square foot lot is valued at $180K. 

for those I used to have a wire type match holder about 2 foot long. 

If it's pier & beam, then that perimeter footing (spread footing) should probably have been 6" - 12" deep.

However, I recommend that you don't touch this method with a 10 foot pole unless you are deeply experienced.

My exit strategy would be to bring the value up and then sell (assuming the comps are predicting greater value then my costs)  Preliminary research indicates that the cost per square foot may be significantly higher then i would be paying, when all in..Thanks!