the pullup/down looks ok, just gpio2 pull-up missing.
So you say that flashing is ok but on restart the connected serial lets your PC go havock?
If it is USB/serial it should be enough to replug the adapter.
again: did you try with a simple sketch like blinky? Just to make sure the esp is ok hardwarewise?
maybe it is just some part of code that magically interferes with your hw-setup.