This is a common problem for those in the phase-out range determined by MAGI. You can take an iterative approach to figure out how much to really need to take out to eliminate the excess contribution with each iteration taking out a smaller incremental amount. Either you'll eventually reach the point where the increment is small enough that the additional gain removed is less than a dollar and does not increase taxable income. You can also take a trial-and-error approach where you try returns of different amounts until you find an amount that is large enough that you no longer have an excess contribution; this is likely to take fewer steps than the purely iterative approach. You can do it as a binary search for the correct amount, each time trying an amount halfway between the lowest tested amount found to satisfy the excess and the highest tested amount that is insufficient to resolve the excess. If you end up close to the upper end of the phase out range you, a third alternative is just to have the entire Roth IRA contribution removed. Finally, you could just pay the 6% penalty and resolve the excess by making a regular distribution after the due date of your tax return but before the end of the year; this distribution would not need to include taxable earnings.
As an alternative to removal of the excess contribution, you can recharacterize the excess to be a traditional IRA contribution (potentially nondeductible) and not have go treat the gain as taxable income since it just moves to the traditional IRA with the amount that is recharacterized.
