These holes in question, does the separator plate have a hole in these locations? If not I would think this is not an issue. In my last post I thought you had 3rd gear. When you say you have 1st and second is this in the manual ranges? Or in D3 or OD range? I will have to take a look to see if I have a set of -3 directions and take a look tomorrow when at the shop. Vince