Discrepancy in appraisal, need genuine advice!

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Hello, I believe I had a major discrepancy in the appraisal, which was verified by an architect, but I wanted to turn here for advice.

The home, calculated by W X L, is 38ft wide, by 40ft long. The home also has a bonus room, with kitchenette and full bath above garage. The home appraiser put the 1st floor as 1566(when calculated shows to actually be 1501). He put the 2nd floor as 1013(shown to be calculated at 1183). He(appraiser) also mentioned the heated sq footage as 2579. Our bonus room(561 sq ft) has a full AC systems, hot water tank, and W&D hookup. Total calculated home sq footage by Architect, not appraiser, to be roughly 3245. 

Now I need to find out if this is correct. The problem is my heating and air unit is a 2 ton and cannot keep up with the house. I need to upgrade it to a 2.5ton. I am also under PMI, and if my home is calculted at 3245, then I can remove the PMI since the value of the home will go up tremendously, considering it was sold to me as a 2500 sq ft home, but in reality it is a 3245 sq ft home.

Please help me if I am wrong here, should I get another appraisal to try to get out of the PMI? Am I correct on saying the home is 3245 liveable/heated sq footage and should be sold/appraised as that?

Thank you