"In retrospect, I should not have used the IRA to fund the premium, given that it included after-tax dollars. I should have used my Rollover IRA to fund the premium."
Makes no difference. Your basis in nondeductible traditional IRA contributions belong to you, not to any particular one of your IRAs. With regard to your basis, all of your IRAs are treated in aggregate as if they were one large IRA.
"I actually compounded my error when I merged the remaining balance in my IRA with my Rollover IRA for simplicity - completing forgetting that the IRA included after-tax dollars."
Again, this makes no difference. All of your traditional IRAs are treated in aggregate. Line 6 of Form 8606 requires the value of all of your traditional IRAs combined.
