Back in January, I had my main board replaced. \[...] So it's unlikely to be a hardware problem unless the memory is bad.
Never rule anything out... I've seen people who had bad hardware replaced with bad hardware, or problems that kept recurring. For example, on my old PowerBook G3 many years ago, I had recurring hinge problems and the power supply card kept breaking off the motherboard, despite having both fixed several times.
There are two kernel extensions I use.
If you can manage to disable both for a while to see if that makes any difference, that would be a good idea. Kernel extensions can cause major problems sometimes.
It'll be a pain, but I suppose it might be worth trying a fresh reinstall. What would be the least painful way of going about that?
You're pretty much on track with your plan except for using Migration Assistant. I don't like MA, as it does not have fine enough control on what gets migrated. I'd recommend reinstalling any applications from scratch and going the all-manual route for importing from your CCC backup. Of course, that requires knowledge of what should go where. For assistance with that, you could post back here with info about what things you'll need to restore, or you could try Googling for the info, which shouldn't be too difficult to find.
Here are the checked login items. Can you identify any of them as being problematic?
Not that I know of. If I were you, I'd remove all of them (except iTunes Helper, which is on that list normally), if you can manage to do without them for a while. You can add things back slowly if you don't have problems. The common technique is to add half back. If you start having problems, remove half of what you added and try again. If you don't have problems, add half of what's left. Keep this up until you narrow it down to one specific item (if there's one causing problems).
Good luck! This sort of thing is never fun.