I basically decided how much top I wanted to end up with, Basically room for a second seat.
Then I cut the center section out leaving enough on the ends to reattach together to come up with the right length of top.
Once cut, I had to cut the rear portion in half the other direction to make it fit the bed rails.
Now take all three pieces and grind them hard, not just scuff but Grind. Make the edges ugly and lower than the rest of the top, kinda like "v-ing" for a weld. I also drilled a bunch of 1/4" holes near the edge to give the new glass something to grab hold of.
I used aluminum strips screwed to the top to set the edges level with each other and hold things in place.
Glass as much as you can without covering the aluminum strips and let that set.
Remove the aluminum strips and finish glassing.
Now, since I made the edges lower by grinding I was able to go back and smooth them off without removing all the glass.
Also glass the inside and whatever window hole you have left.