If you have recently had the tank off you may want to check the control wires (feed and ground) on the coil that is on the front left side of the frame. This should be for the cyl. 1&2 if my memory is correct.
The other two coils (in the void by the ignition switch) are apparently firing so it sounds like the pickups are good. You may have a problem with the ECM not sending a signal to the coil to fire, you need to get to the coil to verify this as well.
If you want to verify voltage at these wires you can do it with a digital voltage meter and a "peak or direct voltage adaptor". You can build a peak voltage adaptor very inexpensively with some off-the-shelf parts. There are lots of you tube videos that show you how to use the adaptor.
Here is a link to a youtube that shows you how to build an adaptor
https://www.youtube.com/watch?v=juhri_NxQcQ or you can get one for about $50 off of Amazon.