Yeah, Clark definitely overreacts at the end of 3rd season. The whole second half of s3 is Clark's worst time, I feel; later seasons he's somewhat justified for being suspicious of Lex, but not then. I really only can attribute it to post-Asylum guilt (and live in hope that one day Clark will realize this!!)

(Hmmm, out of curiosity, how do you think Lex wasn't the mastermind behind the mutants? I've seen a couple other people mention this, and while I love Lex as much as the next raving fangirl, and the evidence is technically circumstantial - the mutants' handcuffs mysteriously happen to turn off right when Lex walks by, and only a little while after they were transferred back to Belle Reve from 33.1? And Lex had the place wired with cameras, and is looking shocked/horrified at the footage of Clark like it's totally different from what he was expecting...if anything I get cranky because Lex is too obviously behind the mutant attack, and not devious enough! Though I don't think hostage-taking was part of the plan, I think he meant them to target Clark alone; and Clark should have been able to neutralize them without anyone coming to harm. Lex's minions do have a bad tendency to take the initiative in the wrong way...)
(this being said, I do find it very interesting that Lex has not once targeted Clark or the Kents since...)

Er - anyway, I'm very glad you enjoyed the story even if it doesn't quite jive with your own take! ^_^