Hi Bryan,
1. They seem to have the part numbers for R and L wing muddled on Page 32/36 that you have shown. I noted this in my build, the correct numbers for R and L are on the previous Page (L wing numbers are in brackets). So check you have the correct parts.
2. If you go to the instructions on that Page 31/36, it says at the end 'Note that they have to be filed to fit inside SB003-5/6'.
I believe this is what I did: trimmed/filed them as necessary so that the assembly sits in correctly against the wing rib.
3. Nowhere in my build did I have to move holes. I used correct sized tapered podgers a lot to ease holes into line, and sometimes it was a matter of assembling or clekoing in a different order. But the holes always lined up. I would regard drilling new holes as an absolute last resort.
(4. When you get to it, I had similar problems fitting the seat pans under the adjustable seats: initially I couldn't see how they would fit, but it was just a matter of trimming/filing small amounts off the pan edges at the points where they were binding.)
PS: While they refer to this part as the 'root wing door support' the door actually pivots on fixtures on the front and rear door columns. When closed, the top of the door presses against this 'root wing door support' closing the air gap there.