You're not being double taxed on the section 1250 gain. It is being taxed at a different rate than the capital gains you received. Because the deduction you got was a regular income deduction it is being taxed as regular income.
You should definitely put the sale of your primary residence on the return. It used to not be a big deal but the last few years the IRS has really started asking about those sales.
You can file a separate form 843 by mail. You need to come up with a pretty good reason for paying the taxes late but it never hurts to ask. Here's a link to the fillable pdf of 843 on the IRS web site.
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