Theres often an issue with misfire showing - ignore it for the time being, its the trigger error you
Can you identify which are the three running cylinders? You should test each cylinder with a timing light and ensure that the pairs of cylinders are correctly firing at TDC and BDC.
Running on 3 cylinders could be down to injectors as well as ignition.
You trace looks fairly solid from what I can see - I am a bit concerned with the dips in the cam trigger - the LM1815 chip senses voltage crossing zero, that might be a source of mis-triggering.
Its also worth taking a look at:
http://www.vems.hu/wiki/index.php?page=InputTrigger/TriggerLogI have also passed this thread to the dev team, one of whom said:
"reference tooth table" (h1) values 22,16,10,4 look strange. They could (and should) work, but standard practice is to set 18,12,6,0 (or rather 0,18,12,6 for quicker startup), and trigger_tooth=04