2000 Honda Accord Code P0306 and more

Hello, I'm trying to help my daughter fix a problem on her car that is complicated by what appears to be some modifications that were done to it. The car was bought in 2000 new, but it appears to have an engine electrical system from a 2007, it has the individual coils on each spark plug and a "V-TEC" marking on it. The check engine light came on after the engine suddenly started running rough during a local trip. The OBD2 card reader called out cylinder 1 as misfiring so I swapped the coil with another one and the problem followed it, I replaced the bad coil and the car improved some, now it has a #6 cylinider misfire code coming up first and then the other cylinders fail also, even code P1399 comes up. I've put fuel cleaner in it just in case she got some bad fuel, no help there. Is there anything else electrical that could be causing the problem? Is it possible the timing chain is worn and causing this?