I believe you mention that you researched a way to determine what the correct cost basis is. If so, you can enter the sale as a normal investment or stock sale without having to go through the ESPP routine. For the short term sale, just pick an acquisition date that is less than one year from the sale date, that will give the sale the correct short term gain treatment. You can do something similar for the long term sale if the acquisition date isn't stated on the 1099-B form.
For the cost basis calculation, you need to factor in the income from the sale that is reported on your W-2 form. That often has to be added to the cost basis reported on the form 1099-B. Often the 1099-B form reports what you paid for the stock, but the remaining discount is included in your wages, so that has to get added to what you paid for the stock to determine the cost basis at time of sale.
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