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I received my MX4 on Tuesday from PartsEngine.ca and installed it on Wednesday evening. It came with the spacer strip at the top to account for the (supposed) angle of the box side rails. I ended up removing them as it would tip the cover brackets on the rails around 40 degrees downward. The box side rail is almost perfectly vertical. Why would Bak add these for a 2016 longbox?
Here are some pictures:
Rail with the spacer removed:
Rail installed on truck. Notice the almost vertical bedrail mounting area
Clamped to bedrail:
These pictures are from Wednesday evening.
I did remove the rails again on Thursday to apply a 3/16" open cell foam strip to the outside edge, but it covered the entire surface and maintained the angle of the rail, just moved in inboard a little bit so the latches engaged more fully.
FYI, I had to space the bike rack away from the front wall about 8 inches to use it with the cover flipped up, but at 20" high (plus a bit of carpet) it still fits under the tonneau.