Time to rivet the frame together. The instructions have you rivet it all together off the plane, which in hindsight wasn't the best idea.
The frame looked perfect sitting on the bench, but as soon as I put it in place, it became pretty obvious that everything had shifted. Instead of the side rails being 1/8" up off the canopy deck, they were more than double that because of the angle created between the front frame and side rails when they were riveted together. The biggest problem wasn't the gap itself, but what having a big gap does to the front of the frame where it meets the subpanel. The extra gap meant that the front assembly was tilted up/forward relative to where it had been when I originally put it all together. That made everything bind and nothing line up. The joys of the canopy!
I tried tweaking parts to get the rails to set down, but nothing worked. In the end I drilled out all of the rivets on the side rail portion of the connecting brace, clamped the rails down to the canopy deck and re-riveted it again. All it took was shifting the holes a very tiny amount (maybe 1/64"). With that, and riveting the upper ear of the front frame to the rail, I was able to get the gap back down to 1/8".
The good news is that the aft portion of the side rails that were originally not very well lined up with the curve of the fuselage have somehow miraculously gotten better. The front joint between the two top skins is still less than ideal and will need additional work though.