Following is my personal opinion, and should not be taken as anything more than that.
I think the story stands on its own without the original epilogue. The altered one actually works better for me, since it allows a version of Lois to survive losing Clark forever and still find a large measure of happiness in life. When you send it to the archive, I strongly suggest using the second epilogue, or you can consider using the slight edit I have made in the last portion.
Her face lit up in a slow smile. "I'm just glad you decided I was worth the wait."
"Me, too, Mayson. Believe me. Me too."
There. Doesn't that look even more interesting?