I answered your last post and again, no offense, I think you are over-thinking things.
We all hear about the terrible 2's, but believe me, 3 can be even harder and it's pretty normal.
They are growing so much, physically and mentally and cognitavely. Sleep patterns change. They test limits. What worked last week can be forgotten history. If you ask a kid this age "why" they are acting a certain way, they are going to say they don't know.
When he's 4 or 5 he may not know why he's acting a certain way.
The whole vaccination thing is a different topic and it's my bet your son would be going through these changes whether he'd had a vaccine or not.
My aunt lived a long, tough life crippled by polio because she contracted it before there was a vaccine.
There was no question I would vaccinate my children against it.
My kids had no bad reactions to vaccines, no fever or extreme crankiness.
That's MY experience. It might not be anyone else's.
My point is, that your son will change eating habits, sleeping habits, temperament......
This age, starting school, puberty and teenage years...
There will be times you think someone body snatched your child.
It happens.
Best wishes.