Doug - hope that this helps. I don't claim to be an expert - this how we did it.
Please measure and make sure that this will work for you before you drill any holes into your plexiglass. We checked by installing our lexan piece onto our 12 sheet metal. It fit great and the holes matched the pre-drilled holes of the aluminum pieces of the 12. We did not have to trim the plexiglass sheet prior to drilling - only a very small amount of filing the two corners and edges as we final fit the rear canopy. That allowed us to go directly to marking and drilling the holes into the plexiglass.
Place the lexan on top of the plexiglass flat on your work bench and align the straight edges of the two sheets exactly - the plexiglass underneath the lexan 'pattern'. Carefully mark thru the Van's factory holes in the lexan 'pattern' onto the plexiglass using a fine felt tipped pen. These marks are where you will drill your holes into the plexiglass. Be as accurate as you can.
Remove the lexan 'pattern' and begin the drilling process. Take your time, be as accurate as possible in drilling exactly where you marked the plexiglass. Use Van's method of drilling plexiglass or whatever method suits you.
If you haven't drilled plexiglass before, I recommend that you research how to do it including Van's instructions at the first few pages of the plans set. Again, take your time while drilling. Best of skill to you.