Welcome to the boards!
You have quite a list so far. Here are some more:
Once Bitten by Female HawkAussie Rules, which has Clark meet Lois in Australia. A controlling version of Mayson is one of the villains. Mild compared to some other stories.
Both of these stories are not in the archives, so I've linked their TOCs (Table of Contents) here on the message boards.
You'll get a redirect link for each post, a quirk of the upgrades of this site.
All of
Female Hawk's Stories are well-written. Trusting Me, Trusting You has both an alternate Lois and Clark having to heal.
Mobile Richard Storiesespecially:
The Fugitive Series
Life in a Different World Series
Queen Lois (Clark ends up in a different alt-world than the Life Series, but gets there similarly as I recall)
One Super Child Can Change a World: A continuation of Mobile Richard's Life in A Different WorldAn alternate version of Part 2 of the Life Series, this one by a different author who had Mobile Richard's permission to write her version; very informative with as I recall references to child abuse, which may no longer be up-to-date (written in 2001)
Stories by StopquitdontThere are multiple stories here, some with physical and others with mental pain; some with both
Merideth Knight's Rest and ReproductionLois causes Clark anguish.
Honeymoon in… Vegas By Sue S.Chris Mulder's
Love Beyond All Measure and its sequel,
Dimensions of Loving.
There are still more, but all of those mentioned by others and these will give you quite a start.
You might also try the Archives' By Site Search or By Random Link for other examples. They're under the Stories Tab in the upper right hand corner. Lots of stories not mentioned here will have some pain for Clark or an alt-Clark although it may not be the focus of the story.