I've never owned a lean burn vehicle. But all the guys on here and elsewhere that have talked about how you can often feel when the car goes into lean burn. So I don't think it's odd that you feel it. But I suspect that what you're describing is maybe an excessive feel. I think that, given that your code 12 was for the EGR system and that it is not recurring since you clean the EGR, you must have solved that problem. But perhaps you had two problems confounded together. So you're left with this second issue for which you're not getting a code.
Some parts of your posts I cannot understand. Are you saying that you're still using the California ECU even though you've otherwise converted to a 49-state lean burn system? If so, I have to imagine that would be your problem right there.
If you have not cleaned out the EGR ports as thoroughly as you could have, or if you have some kind of intermittent failure with the solenoid or other parts of the system then that seems like a reasonable suspect.
At any rate, you should search carefully on this website using the search function in the upper left-hand corner. I searched for cleaning EGR passages I found a number of hits. A good one is this one from an old member who was always really thorough with his vehicles. He had an HX, but I would imagine most aspects of the lean burn system on the HX are the same as they were on the VX, except for the codes and the sensors. But I'm just guessing. Here is the link:
https://ecomodder.com/forum/showthre...ean-30057.html