Firstly removing the EGR plug will prevent it opening but if it is stuck open anyway it will have no effect, also removing the plug will disconnect the position sensor as well and may confuse the ECU. If the EGR is stuck closed it should not affect the low down running and should only affect the emissions at higher revs.
I would NOT recommend using WD40 on the EGR as this will not have any effect on the carbon deposits and will probably just gum it up further (WD-40 tends to dry to a sticky goo anyway, but given the heat of the EGR it may well turn into superglue). Use a carburettor cleaner if you want to try and clean the EGR. Otherwise make a tinplate or other thin metal plate to fit under EGR and block the hole completely, only use this for diagnosis, don't leave it in place permanently.
Misfire may be due to ignition problem, try disconnecting and replacing the 2 pin plug from each ignition coil in turn with the engine running at tickover (its only 12volts), if the removal of a plug has no effect on the misfire then suspect that coil pack or sparkplug, if it makes the problem worse with the plug disconnected then that coil is probably OK. If you do have an sparkplug or coil problem then you may also notice some 'pinking' when going up hills or accelerating.