It really is a wonderful premise. And it makes a lot more sense than clones or reanimation or evil doubles. I want to see what you do with this now, because there are so many ways you could take it.
Is Lex permanently disabled or did he make a complete recovery or is he somewhere in between? What happened to Mrs. Cox? Did he "reach out and touch her" while they were both incarcerated? Or is she in witness protection somewhere? Did he and Lois sign the license in this timeline? (If they did, they're married; the ceremony is only that, a ceremony with no legal impact.) How free is Lois? Does she know about Clark's "other job?" What's the status of the Lois and Clark relationship? Since Lex isn't dead, his will wasn't read, so has Arianna Carlin entered the picture? How is Intergang doing these days? Were they held back by Luthor's influence, diminished though it might be, or have they forged ahead with their plans? How was Clark personally affected by saving Luthor but with injuries? Is he upset because Luthor lived or upset because Luthor was hurt or not at all? How did Lois react to this turn of events? Did Franklin Stern still bankroll the Daily Planet's rebuilding? Did Cat leave after all? (I hated to see her go! She was my favorite secondary character.)
So many ideas, so many questions, so many options! I'm sure you'll find a path that will make sense and enthrall your readers. Post again soon, okay?