For clarification, a header has no cat, a manifold does. You also only have 1, so it's not "headers" or "manifolds".
Deleting the 3rd cat will do nothing sensor wise, as there aren't any sensors after the O2 sensor at the bottom of the manifold/header. It's only the pair of cats on your manifold that affect that. I'm having a hell of a time understanding you too.
So what you have done, if I understand correctly, is:
1: Removed 3rd cat
2: Replaced the original manifold with a new OEM manifold (NOT a header, right?)
3: Replaced one of your O2 sensors (which one)
Really we need the code to know what the actual problem is without wild speculation that could be totally wrong. But you're also saying MIVEC doesn't engage. How do you know? Butt dyno, or are you measuring the electric current to detect the MIVEC control?
If it is related to the emissions system, it will tell us which O2 sensor it is from the code if one of them is bad. Being at 212k miles, it wouldn't be odd for you to be on your 3rd set of O2 sensors (Installed at 0, roughly 100k, and roughly 200k)