Instead of using (Do After x Seconds), try creating a Number Attribute called Game Timer (or whatever you want).
Initialize Game Timer to have a value of 0.
Now, set up a (Do Every 1 Second) block:
If [not paused]
Increment [Game Timer] by 1.
This means that the timer will not go up while the game is paused.
Now you can set up your waves to come in once Game Timer = whatever number you choose.