"How do I apply the lifetime exemption without paying the $50,000 the 709 says I owe?"
I suspect you may have failed to insert your credit amount on Line 7 of Part 2 (page1).
See page 18: https://www.irs.gov/pub/irs-pdf/i709.pdf
If the task appears to be too daunting, there is software available that you may find useful, now and in the future.
See http://www.puritas-springs.com/products.aspx