Can anyone tell me where to look for the marks on the pinion flange to line it up correctly with the differental flange. I've searched but came up empty. Anyone have any pictures of this or possibly the FSM that describes it? Thanks guys.

99 2wd 4runner.

 

No alignment is usually needed. If you are worried about it, paint a mark on the flange and diff. and call it good. All that needs to be done is ensure the driveshaft itself is properly phased:
http://www.4crawler.com/4x4/CheapTri....shtml#Phasing