IRS asked for forms to substantiate 1040X, I sent them, but I got a follow up letter saying they haven't been received

First off, let me clarify this issue isn't because of Turbotax but because TaxAct messed up my 2019 1040X amended return (it didn't send the corresponding form 8959 and 8960 updates).  This is why I threw in the towel after many years with them and am here now.

 

I first learned of the issue when I got a letter late January 2021 asking for me to send those two forms.  When I went back to TaxAct and printed the forms, I saw differing values vs the original 1040.  However the IRS had the original values before I fixed a cost basis reporting error.

I learned this after spending 3+ hours on hold with the IRS and finally getting to someone who could pull up my return to confirm the old numbers were there.

 

I asked if there was a fax number for sending the requested updates, but I was told not, so I mailed the forms (uncertified, unfortunately).  A little over a month later I received another letter asking me to pay the IRS the difference from my original and amended returns because they didn't receive the forms they requested, and that if I wanted to appeal I had to pay first.  So I ended up going to the IRS online payment system and paid that amount using the following classification:

 

Reason for Payment: Balance Due

Payment Type: Income Tax - Form 1040

 

My question is whether I did the right thing with this payment, and if not what should I have done?

 

I assumed my mail is stuck in a trailer and won't be seen for weeks, but ultimately I want them to get my updated forms and for that money I sent to be returned as an overpayment.

 

Does anyone have suggestions on how to fix this?  I tried calling the IRS and the taxpayer advocate services mentioned in the letter, but both kicked me off right as I got in the queue because too many people were already there...