01 Outback timing belt, Help!

Well I replaced the water pump and timing belt using a lot of information from the archives and member suggestions but it's not right. After installing the pump and new belt I turned the engine over with a wrench a dozen or so times and got no interferance so I started it and it runs rough and noisy. After stopping it I turned it manually to line up the crank mark and both cam marks were still lined up. I think I lost the basic crank timing position while it was apart (at least I hope so) If I remove the belt again how can I be sure that the crank is in the right position before installing the belt? Any other suggestions?

lost the timing position? There's a mark on the crank sprocket you line up with the mark on the oil pump, marks on the cam gears you line up with the timing covers, and marks on the belt you match up to them. The fact that it runs means you can't be off by more than about two teeth which probably means no valve damage.