Stage 3 is probably the easiest, except for Optical Camouflage, which is an auto bomb for me.
Non-cards are simple, just get away from the metal fatigue bullets before you start moving through waves.
Trauma in the Glimmering Depths:This is best shown with a picture

See the wave with the red line through it? Look at that wave, and position yourself about where Reimu is in the screenshot (maybe down very slightly in this case) in relation to it. The metal fatigue bullets are aimed, so slowly stream as shown with the yellow line. See the red/yellow lines at the top of the screen? It's going to look just like that in a few seconds. This might even be exactly the same every time, but I've never bothered to check.
Kappa's Great Illusionary Waterfall:Go right and let the bullets come to you, then move left through the "waterfall." You should be all the way to the left before the next wave comes. Do this one just like the first, except in reverse. Repeat until capture.
Spin the Cephalic Plate:There might be a better way to do this, but I always go to the right wall and sit there for two waves, then quickly jump to the left and stay there for two waves, and back, etc. I use ReimuA, so I can actually capture it this way. If you aren't using homing attacks you might want to do something else.
EDIT: oh right, I made a
Replay too. Everything except Optical Camouflage (which I bombed).
EDIT2: hurrrrrr