Complaint sub-issue: Billing problem

I recently purchased a new vehicle through a dealership at which point the vehicle was financed through PNC via the dealership. Provided to me at the time of vehicle purchase was the method, per PNC, to set up automatic draft. Since all of my other bills are automated I opted to go this route. Per their instruction I provided the account information along with a payment in the form of a check. A few months later PNC calls me saying my payment is late and they are going to assess late fees, however to stay current I make payment over the phone ASAP. When inquiring as to the status of my autodraft the representative informed me they had no information on file. I requested the form to be mailed to me again so I could resubmit. 

I never received and again received calls from PNC that payment was overdue so I immediately made payments. I made multiple requests to receive information via email since I frequently spend weeks/months at a time out of town for work but my requests were denied as that is not a capability of PNC at this time. I could not even set up an online banking account without a pin that had to be mailed to me, which I would not receive for weeks/months because of my travels. 

Again I request autodraft paperwork and upon receipt I resubmit the paperwork for autodraft with a payment in the form of a check to keep me current. I received no correspondence of any sort so I was led to believe that they actually processed the autodraft and everything was working as planned. Approximately 2 months later I receive a letter in the mail proclaiming my account was 90 days past due and they were going to repossess the car. I immediately called and made payment. Within 48 of making payment I find my credit has been hit for a late payment when all of the while I was under the impression I was on automatic draft. 

After further communication and investigation with PNC they claimed that by the time they went to process the autodraft paperwork my account was past due. This seemed odd to me since I included a payment with the paperwork. However, since it took over a month for them to process the autodraft by the time they did get to process my account was past due so they simply threw away the paperwork and never informed me ( happened twice ) that they were throwing it away and not setting up the autodraft as I was expecting. 

All in all this has been an overwhelmingly frustrating experience due to their lack of care and inibility to work with me. On top of this, their archaic methods of business and communications seem to me that they are basically setting a trap for unsuspecting consumers accustomed to efficient banking practices ( ie practices done instantly online, communication via email/text, etc ... ) in the attempt to profit. 

On top of all of this, there may be considerable monetary stakes for me in this matter. A month prior to this credit hit I put {$47000.00} down a house that will shortly be under construction. Due to this scenario, my credit score has taken a substantial hit and I may not be able to get financing upon closing, at which point I would forfeit my down payment. If I am able to secure financing at my much lower credit score, it is safe to assume the increased interest rates and rising cost of PMI will, over thirty years, cost in the hundreds of thousands. 

My credit report clearly indicates I have NEVER missed a payment and would have never missed this payment if PNC had followed their own protocols, which in and of themselves do not belong in the 21st century. They made no attempts to communicate with me and no attempts to rectify the known issues I was having and clearly took advantage of me as a consumer.

I am seeking advice on how to best approach this situation and get the hits on my credit score removed if at all possible. I truly do not believe I was at fault as I tried to set up automatic withdrawals on multiple occasions and was never made aware they did not set it up. Any and all help in this matter is beyond greatly appreciated. 

Thank you for your time.