Hello Colin, could it be because the exhausts are completely seperated that when you block one exit off on the same back box it is creating to much back pressure which would in turn affect inlet manifold vaccum and make it run uneven (engine not breathing properly )

You say it has intermittent missfire, coils and plugs ok ???
Can you watch your pre cat lamda voltages through live data and see how they are switching,it will give you an insight to how the mixture is at idle.

Looking at the gas readings at idle without you blocking off the pipes the hc are 0 so doesnt seem like a coil or plug missfire, but cats can mask this to a degree.

Exhaust system sound (no minor leaks)??

Check inlet manifold vaccum with a guage , good engine 21/22 inches of mercury or if you have a smoke machine give it a go .

Could be a dirty hot wire on air mass meter , can make the engine run a little lean at idle.

A few things to have a go at .