OK, I have a better view of your picture on my laptop....the screw holes you are referencing mate with the Y support inside the ski.....the top deck holes line up with the top of the Y, the Y support leg should be held in place by the rear deck cover and a nub in the hull so it doesn't flop around...I assume you also put the rear strofoam float piece back up under the rear deck? as the Y support kinda rests against it as well....once I put the top deck on, i used an awl to get the pieces lined up and installed the screws.
Just for the sake of completeness, 2 things:
1) The 2 screw holes indicated are lined up with 2 screw holes in the Y shaped support bracket inside the ski. The screws go into plastic nuts that fit into the Y piece...THOSE NUTS CAN FALL OUT, I siliconed mine into place so they wouldn't fall out anymore (PITA)
2) The steering problem was solved by restraining the steering cable properly. The steering cable has indents in both ends (front steering yoke and rear through the hull). The one in back through the hull was the tricky one...you need to re-install the original 2 (or 3) rubber washers to fill the space through the hull before you put the split 2 piece plastic retainer bracket (which has the plastic nubs that hold the steering cable) back around the steering cable and bolt it back in to the back of the hull.....took me a while to figure that out....my guess is you (like I) have / had your steering cable pushed too far into the hull. Once I pulled the cable out and realized how it works and what I did wrong upon the initial re-assembly......the steering was fixed. Hard rights, hard lefts and dead straight were all EASY to set after that.