You're right on the pistons...JE's aren't positional front/back...at least mine weren't...what rods are you using?...if stock then the 2 dots on the rod determine which direction the rod/cap go...
Drivers Side/left bank/Cyl #1 , #3 , #5 – bumps/dots face rear of engine
Pass Side /right bank/Cyl #2 , #4, #6 – bumps/dots face front of engine