You've given us a very fascinating and ominous A-plot here, Janet. Not only is somebody testing Superman, but the whole scheme is so elaborate, too. So thorough. Whoever is behind it has a lot of resources at his, her och their disposal. Lex Luthor, probably. Possibly Billy or Mindy Church, with or without Intergang.
I can feel how you are building your story towards a huge confrontation and an explosive climax. I wonder - will whoever is testing Superman learn about Kryptonite? I don't remember - do Clark and Lois in your story know about Kryptonite themselves? Probably not. Will Jason Trask get involved?
The one bad thing about Lois being as "super" as Clark is that she will be just as vulnerable to Kryptonite as he is, so she can't help him if he is exposed to the mean green rock. On the other hand, Lois could most certainly and definitely be the key to the defeat of whatever criminal is behind the Superman "tests". When this criminal has learned about Superman's limits, he could set up two catastrophes in such a way that Clark would be unable to deal with more than one of them. With the correct planning, the criminal might feel sure he would get away with his evil schemes. However, if Lois had kept her own superpowers a secret until then, this could be the crucial moment when she finally reveals her abilities and helps Clark nab the villain(s).
The A-plot has so much potential, and it will be fascinating to see it unfold. However, Janet, as a B-plot junkie, I hope you have some plans for Lois and Clark's personal lives, too.
Ann