OK so I messed with it today and it looks like the timing belt skipped a tooth. When you look at the cam sprockets from the left side of the car at TDC the upright arrows were about 11:30. Oh well.

I managed to get the crank and cams aligned again but it still clicks when I put it back together. The belt has 100k on it so go figure. It must have bent a valve.

When I changed the rotor I pushed the car in fourth gear to get the rotor to spin a bit. This might have tensioned the belt weird and when I started it it skipped. but who knows.,