I had something similar on my MR2 and the cambelt was out by a tooth, don't think that would be your problem though tbh.
I don't have a petrol, but could it be a coilpack?
Don't think its a coil pack, had 2/4 die on me a few months back so changed all 4 and the plugs as well
Hmm yes fuel filter, I have noticed when shes nearly empty it runs really rough yet when I pull out of the petrol station with a full tank shes smooth as silk for a good few miles.. does this sound like a fuel filter problem?
Could be worth doing it just to see..they're not expensive and don't take much to change them.
Could also try some injector/fuel system cleaner.
Put the standard radio and cd changer in it and getting pissed off that no one wants to buy it!!!!!!! Would of thought at £2950 it would have been snapped up!