chemie,
Not quite sure I understand your question. Hope this isn't getting too frustrating. I didn't need to sand any of the ply, or if I did, it was VERY little. The 1/4" stock is on top, and it gets tapered when sanded. Is your 1/4" stock on the edge of the canopy floor? I think after you have to hatch in place, you will get an idea of how much gets sanded. When you post a pick of your hatch, maybe we can see what's going on?
My end cap was not real strong, so I used epoxy to glue it together. Probably not necessary, but makes me feel better. I would guess that Sig figures that when the canopy gets glued on, the canopy holds the end cap in place.
And for what its worth, I did not like the idea of cutting the tube, but that's just me. And, I plan on mounting my tank hatch, and then putting the covering over the hatch seams to keep it good and sealed. I will probably use a small amount of silicone at the seam on the firewall. Should still be able to easily cut the covering and silicone if I should ever need to remove the hatch.