The amount on line 6 of Form 8606 is a user-entered value. If it's wrong you can go back and change what you originally entered. Line 6 is to be the sum of the year-end balances of traditional IRAs only, not Roth IRAs. From the transactions that you mentioned, it seems like balance in traditional IRAs at year-end would have been zero.
Also, it seems like the rollover to the Roth IRA and the conversion to the Roth IRA were separately entered as ordinary Roth IRA contributions under Deductions & Credits. Nothing about the amounts rolled over or conversed is to be reported under Deductions & Credits. These are to be reported only in the section for entering Forms 1099-R.
Nontaxable amounts distributed from retirement accounts are not subject to penalty.
