Have you made sure that you are fitting the correct cover side on the wheels? The 2 sides are different in shape with the non drive side much more concave than the drive side. You will get some warping but this can be resolved with double sided tape in the underside or with small cable ties which you will need to drill 2 small holes either side of the spoke where the warping is. Only issue with cable ties is the hassle of cutting them off if you want to remove the covers.

I had a similar issue when I had a cover made for my HED Stinger 6 wheels (similar to 404 depth). When using the supplied screws, there would always be a spot where it was warping. My understanding is that there are two solutions:
1. Use a longer set of screws, which will not force the cover on as tight, thus eliminating the warp. I believe you can get that longer screw set from wheelbuilder.
2. Forget using the screws, and use good quality electrical tape (3m) to secure the cover all around the edges. This is what I ended up doing, worked fine.

Cheers

Try flipping it inside out. Sometimes it changes the dish of the cover just enough to get it to set right.

Also, I never was a big fan of the hardware. I always taped mine with 3M 33 electrical tape. That also seemed to reduce any bulges/warps or whatever you want to call them.

Well I got the cover on with hardware tightened and there still is a significant warp on the non-drive side but it looks better than before. It lays flat on the Zipp carbon fairing on the outside of the wheel but the warpage more towards the center of the wheel. I'll take it for a test ride tonight. I may have to try the zipp tie method on a few spokes around the wheel but not sure how i'll locate the spokes now that they are covered to drill the holes.

If there is still a warp, then ditch the screws and tape it to the wheel fairing.

In my experience there are two things that could cause warping. If the cover is cut to the right size and sits flat on the rim before you put the screws on then using electrical tape (Scotch Super 33+) instead of screws should fix the warping. If the covers are cut too small then that could also cause warping and there isn't really anything that can be done to fix that. I would assume wheelbuilder knows the proper size to cut their covers to for a popular wheel like a 404 FC, though, so my guess is that it's just the screws that are causing the issue.

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Zach McCormick
Catalyst Cycling
http://www.catalyst.bike

update: last night I got the AJ cover on as best I could. It just wont lie flat on the not drive side no matter what I do. I dont know if its just the design since it lies on the wheel fairing and there is a gap between the spoke and the cover in its design. I was able to do a test run on a local TT and there were no probs other than I needed to move my Garmin sensor further back on the chainstay since the cover was rubbing on the sensor arm. I'll have to glue/tape a magnet on the cover now since I dont want to take it apart again. There is quite a bit of warping on the non-drive side still but it works as it is ok no rubbing and no noise. I'll probably throw some 3m tape on it just to be safe.