'98 Honda Passport/Isuzu Rodeo timing belt

[olderguy]

I replaced my belt even though it was okay. It ran fine but I had forgotten to re-torque my new water pump and it turned out to leak. After awhile I went back in and did it over. By that time the marks on the belt were gone. Thinking this would cover everything I merely made marks on the belt and the various sprockets, but did not align them with the timing marks. What I didn't realize was that the cam sprockets were not "snapped" to their positions (I hadn't had this experience, since the first time I aligned everything before removing the belt). When I released the tensioner, they snapped to whatever
position was closest. When I tried to re-align my marks with the various sprockets, they would no longer align. I realized what had happened and read the book, carefully aligning the crankshaft pulley's notch with the oil pump mark and rotated the cam sprockets until each "snapped" to where their marks aligned with the marks on the valve covers. Then I simply re-installed the belt (now the marks I had made could be made to align with the cam sprockets but not with the crankshaft sprocket. I'm not sure why. As I say, it had run fine after my first installation. When I re-started it it ran really badly--it felt like half the engine was not firing. I took it back apart and went through it very carefully, making sure that when the crank sprocket was at the mark, #2 piston was at TDC; went through the cam sprocket rotations until each went 9 steps and back to where it snapped to the right mark. Put it back together with no change. I haven't done anything to any other parts. Any suggestions? I am assuming that crankshaft positon + Camshaft position is all there is--am I wrong? Could I still have something out of phase?