My thoughts are that the engine is under maximum strain, putting out maximum power. With your mods, perhaps this gives :-
1, higher than normal boost in the inlet manifold
2, blacker than normal exhaust
Perhaps you could try and turn your boost down a little and see if it makes a difference.
Could it be EGR valve issues post delete?
Does the exhaust have a sensor in it? Could this be getting/ have become fouled?
Maybe the link wire will help narrow it down, maybe it will complicate things.
The thing is, I would think with your mods, you're the best bloke to sort it as anyone else will likely want to put it back to a standard set up before proceeding.