There is no way to treat the rollover and conversion in any way other than as I previously described. The tax code prohibits you from applying all of the basis to this Roth conversion.
If the administrator would not issue two direct rollover checks, the only possible option would have been to do a direct rollover to a traditional IRA of the pre-tax portion and take a cash distribution of the after-tax portion, then complete the rollover to the Roth IRA indirectly, if the pension plan would permit splitting the distribution in that way. See IRS IRS Notice 2014-54: https://www.irs.gov/pub/irs-drop/n-14-54.pdf
