I had the same issues on that assembly. One of mine fit perfectly, the other gave me some problems.
What I did to solve the problem was to cleco every other hole on -903 and -904 starting in the middle of the pieces. I then laid the assembly on a piece of glass keep on my workbench to check for a warp. Indeed, there was a small "wobble" or twist.
Section 5.13 (Page 05-14) in the manual talks about twist and fluting. It says "any twist in the part can be ignored". It also says, "...It is normal for light pressure to be required to hold a twisted part flat on a table. Fluting does not remove twist from a part."
With this in mind, and clecos in every other hole, I then twisted the assembly with my hands ever so slightly in the opposite direction. I laid the assembly back on the glass at it was perfectly flat. At that point, I installed the remainder of the clecos. The assembly stayed flat after the balance of clecos were installed.
The next challenge was getting -913 to fit properly around the assembly. Be sure to start by putting the clecos on the front portion of -913 as per the plans on page 09-17. I had to work with -913 a bit to be happy with the fit.
While I don't have the experience of many here, a couple of things I've learned with the -14 are:
1) If you're having trouble getting something to fit properly, put in all the clecos before deciding you have an issue.
2) If the holes don't line up, you've probably done something wrong
My guess is that you'll have to work a bit to get -913 to fit like it should.
Best of luck,
Dues Paid for 2018
Getting Ready to Close Wings