Misfires could be fuel, spark or timing. Any particular pattern to when the CEL comes on (after a hard pull, sitting at a light, etc)? Is it only P030X codes? Any P0300 codes?
Looks like you may have addressed the fuel situation (however, if you used aftermarket injectors…). That leaves spark and timing. I would give the coils a good visual inspection for signs of carbon tracking. Also, if you have not changed the spark tube seals, there could be oil in the spark plug tube and that could cause a misfire. If you are getting P0300s it may need a deeper look into the timing. Not a toyota guy, so not sure how their VVT works. Also check your plug gap, if you have not changed them ever, it may be time.
Good luck. Hopefully you can catch it when it is not behaving and figure it out.