1. I agree with Critter-3 on this question. It doesn't matter that the conversion was don in two separate parts.
2. For tax purposes, the distributions from the traditional IRA are treated as if they occurred simultaneously on December 31. If the 401(k) will accept a rollover of the remaining balance in the traditional IRA with the distribution from the traditional IRA occurring before year-end, all of the $5k converted to your Roth IRA will consist of your $5k of basis in after tax contributions because your traditional IRA balance at year end will be $0. None of the money rolled over to the 401(k) will be after-tax basis. The important thing is that the amount you converted to Roth is no less than your total basis in nondeductible traditional IRA contributions, otherwise rolling the balance of your traditional IRAs over to the 401(k) will impermissibly include some of your basis. By first doing a Roth conversion of an amount equal to your basis, you've guaranteed that no basis is rolled over to the 401(k).
