Try closing the shut-off to that toilet and see if the noises go away. Sometimes the fill valve in the toilet can create all sorts of noises in the house. By closing the shut off, you've isolated the toilet from the rest of the system. If that makes any difference, get either a Fluidmaster or Korky quietfill and replace the old filler in the toilet. If the noise continues when that shutoff is closed, somebody else will have some ideas.
Re the bladder tank...did you check the pressure prior to turning the pump back on? It should be 1-2 pounds less than the turn-on pressure of your switch.