What customs? You only pass through customs when you enter a country, not when you leave.
Switzerland is in the Schengen area so there are no customs or even passport control anyway. You will only need to go through security.
90 minutes prior to take off should be fine. 2 hours if you are the nervous, gonna miss my flight type.
It often rains in Amsterdam all night, yes ;-)
Where is your hotel as getting a train might not be your best option?
Check in, Print your boarding passes, Take a prebooked taxi. Leave at 5:00am. You will have plenty of time.
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