Retirement tax questions

I accidentally put too much money in a Traditional IRA in 2018 (didn't realize I didn't qualify for the full $7k due to amount of income over threshold on worksheet) , and realize I didn't get the advantage of pretax contribution (and don't want to be double taxed), and have prepared to send in a late 8606. I have other Traditional IRAs, so I don't think I can do a back door IRA.

1) will I need to pay $50 to file a late 8606, Or should I just see if the IRS sends me a bill?

2)The non-deductible portion is approximately $5000 of a $10000 Traditional IRA. I am 60 . Is there anything I can do other than withdraw it in say 1 or 2 years? Is it complicated to take a traditional IRA and identify it as a prorated amount deductible/ non-deductible? Are there any references you can provide me that I could review? I'm guessing there is nothing I can do to convert this to a roth, unless maybe I were to combine my traditional IRA accounts , if even that would work? should I figure out my IRA's value before and after the deposit for proration purposes? I'd also prefer not to resubmit an amended return for 2018, and have it scrutinized