how far was the marks off from TDC? Either your pump has the alignment peg in the wrong place, the crankshaft was rotated slightly, or (iff off more than 50-60 degrees) you have the balancer out of alignment (one hole is offset, so usually you will find that you have one bolt left over, because only 5 would screw in instead of 6).

__________________
Don't ask me, I'm a shop-owner by default