So the missing tooth passes the sensor 90deg ATDC?
That means that the missing tooth passes the sensor 90deg BBDC.
So unless you're on an odd-fire engine this will mean that the trigger will be 90deg BTDC of one of the other cylinders.
What you need to do is work out which cylinder is on its compression stroke when the slot is level with the sensor, and use that cylinder as the first in the sequence. Just because your engine has (for example) a firing order 1, 3, 4, 2 it doesnt mean that you have to setup your VEMS in that way, you may be 180deg out so you'd have the sequence 3, 4, 2, 1