Thanks for guiding me through all of this. Your instruction have allowed me to get the same amount I calculated for a refund. I will wait a bit longer to file my amended return, because I want to make a few phone calls first.
Since my last update, I have spoken many times to both my employer's payroll company, and the HSA bank, and both sides are unable to help me. The HSA bank says that since I am NOT the primary account holder for my wife's FSA, I am allowed to contribute to my HSA, even though I am listed as a dependent on her FSA. Therefore, my maximum contribution limit is $4,150, and thus they will not correct my 1099-SA to use distribution code 2, excess withdrawal. I have contacted my employer's payroll company, and had a conference call with the HSA bank, and both sides said that there is no way to pay the $5 maintenance fee to withdrawal the full amount of my contribution.
Going forward, I'm going to contact the IRS about my situation, and then file an amended return afterwards.
