You can run the engine fine with the egr unplugged via the vacuum pipe, I have done for nearly 8yr with no affect on the engine even with the mot's carried out.
It could well be a sticking Axel in the fip pump. There is a big magnet surrounding the throttle axle in the pump and debris can collect on it and jam momentarily.
On mine it occasionally does not respond to the pedal, I bang the pedal down a few times and it'll come back to life... This may not be your problem but there a few of us that have had this.
There is also the turbo waste gate that could stick but this is activated by itself and there are no outside electronic influences but if it was sticking it would either stick at cold temps, hot temps or stick all the time.
The problem is when it's completely intermittent it's a real barstool to track down