What I did in similar situation is override the % on line 10 of part I of form 8606.  You have to do this every year an amount is taken out of an inherited IRA, when client has basis in traditional IRA.  I file these returns by themselves because you have to turn error checking off e-file because of the override.

It sounds like you know the amount desired on 1040, line 4b so just keep track of calculations in case ever questions.  The % override has to be calculated based on existing traditional IRA 1/01 balances only.  But the software wants to take the non-deductible amount against all IRA distributions.  This also results in the correct carryover of non-deductible basis to next year with only one over-ride.