There are no MAIN shut off valves in your plumbing system......ONLY valves to isolate water heater.
Even IF water heater valving was incorrect you would still get water flow from COLD side of faucets, shower and toilet you just wouldn't get any flow from HOT side.
IF water heater valving is correct.............then water heater tank has to fill before you will get flow from HOT side but you should still get flow from COLD side.
City water inlet check valve bad......no water at all
But with water in fresh water tank, pump on should get water.
Can take a while to purge air from system.
Also......faucet aerators could be clogged but toilet should have water.