I changed some of the rules a bit:

1. On the individual level runs you can use any starting layout.
2. In the full game runs (The Virus + Miracle in danger) timer can be paused during loading screens and when switching between levels. This is to reduce time loss caused by having slower computer.

If you think there are mistakes in these changes please reply below.

so every final cutscene u pause the timer and start it again when you can click again?

Yes