first you need to determine if the problem on the 2 cylinders is due ot them not firing (no sparks)
visually check for sparks on the plugs.
assuming you dont have sparks and you have replaced the coilpack, ht leads and plugs, you can assume the problem is either a broken LT input signal wire from the ecu to coilpack, or a fualty ecu.
the coilpack has 2 LT input pins, each one has a wire that goes to the ecu. one of these may be damaged, this would mean a coiled pair of cylinders would not fire (e.g. 1&4 or 2&3). do a continutiy test on both these wires from coilpack to ecu. i cant remember the ecu pin numbers and its home time now so you'll have to search the forum.
if the problem is not sparks, it will be injectors. searth the forum, this is a common fault on the 1.6 and there is plenty of info in previous threads. check the resistance of all injectors.