if you have changed the coils and not the plugs, the problem might be in the plugs or the wiring to the coils - the wiring might be shorting... do you get the worsening condition when the car is under a load - say going full throttle uphill? in other words, regular driving, misfire, no codes, uphill under load - codes, and check engine light...
before going into the more sophisticated issues, as the shafts or whatnot, you should completely rule out simpler issues, like oil in the plugs, or shorting wire harnesses, or other electromechanical issues... Have you had a chance to reset the codes and see if they comeback? if you are doing this kind of work yourself, you definitely need INPA software package, sold by a dude from romania - many of us have bought it...