I think the writing is fine as it is. To me, they sound like the conclusion of the reanalyzing: She was reanalyzing, and now she knows something: X cannot be true. Y should be true.
In fact, "should have been cooking a bigger plan" makes it sound like it is too late to do that now. Similar to "Joe should have been saving for retirement", or "Kathy should have been watching her sugar intake". It sounds like they should have been but did not and now it is too late and they shall face the consequences.
If that is what you want to imply, use "should have been".
On the first, "couldn't be" and "could not have been" are mostly equivalent, but if the ramifications are still ongoing or the secret of the true motivation will have further consequences, I would use "couldn't be". The motivation is still operative and we need to find out what it is.