Did you do a quick check by touching the downpipes ,before they get too hot, might give you an idea if one cylinders not running, but as you say start with the plugs and then while doing that check for a spark at each plug before putting it back in ,ive heard people having trouble with coils going so could be your prob,hope this helps and good luck.
Was it running ok before you fitted can?Putting an ohmeter across the coils will tell you if they are ok while you have the tank off ,my manual for a 2k triple quotes the resistance reading of 0.7 to 0.9ohms,dont know if 2003 model is different.
