If you have time to take it all apart again, wel all the power to ya. I would look at other things before I go and take the front of my engine apart again.
Those marks on the oil pump gears mean absolutely nothing as far as re-assembly goes, so don't bother with them.
Did you tighten down your valve cover too tight? It only needs to be snugged down with a 1/4 inch ratchet. You also may want to consider setting your valves at 7 & 11 if you haven't already done that.
Good luck with whichever route you take,

Tye

1985 Toyota $Runner - Locked front and rear, Chevy's in the rear and rears up front, 36" Iroks, blah, blah, blah........
1993 Nissan Pathy
2002 Yamaha Wolverine