I pulled it apart again and re-timed things. I used the crankshaft pulley timing marks vs the timing belt pulley timing mark and that seemed to fix things (though the timing belt pulley mark does seem to be off now
). I got it all back together and I got one more engine code, P1298. This seems to be a bad electronic load detector sensor which is
another common issue. Very easy fix and costs ~$30 at a dealer. One more thing to add to the list. Oh yeah, the power steering pump is also whining like crazy when I turn the wheel... meh. I'm ready to be done with this car.
On the up side. I got the rear passenger door to open up. It was stuck closed. I also repaired the driver's side door switch which had been pushed into the frame. I'll probably get a replacement switch for that as I hear it'll probably just get pushed in again.
So, still plugging away at fixing the Civic.