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Jon,
What I do for belt alignment/pump alignment:
First, remove timing belt from sprockets.
2nd, I set TDC with a dial indicator. If your head is still on, then you can use the timing window in the transmission. USUALLY TDC is with the flywheel mark JUST AT the beginning of the window (before the actual "0" mark).
I then take a dremel with cutoff wheel installed and make a cut in the crank timing belt sprocket and a cut in the front crank seal retainer that line up with each other. I put these cuts in a way that you can see them very clearly from the top. Now you will always know where #1 TDC is at the crank.
Now, line up the factory dots on the intermediate shaft with the crank sprocket at TDC still. You can do this one of two ways. If you have the oil pump in already, then you can fiddle with pulling the intermediate shaft out just until the teeth don't engage with the pump any longer, and then make a tooth jump CW or CCW which ever way you need to, or you if you have the pump out, you can pull it down until the teeth no longer engage, and then turn the intermediate shaft CW or CCW. What you want is the dot on the crank sprocket lined up with the dot on the intermediate shaft sprocket and the slot in the oil pump parallel with the crank. You get the hang of this very quickly and it only takes 1 or 2 tries after you are a pro!
Now with the dots lined up, and the oil pump slot parallel with crank, I whip out the dremel, and make a slot on the intermediate shaft sprocket, and a slot on the front crank seal retainer once again that line up with each other and are visible from the top.
If you don't run a timing cover on the bottom, you can now line up all your sh*t without ever having to jack up the car, take the wheel off, or even take the crank pulley off!!!