The pet store said to only let him out of his crate 3x per day?

That isn't nearly enough.
If you are going to crate train, he should be allowed to play after he uses the bathroom in the designated area and he should be allowed to try and potty at least once an hour and no less than once every two hours which is pushing it at his age (decreasing as he gets older).
Wet food can't be left out too long.
It should probably be refrigerated after about one hour of being out.
Welcome to YT and congratulations.