I live in Hawaii and it rains and windy all the time. I do not have the factory gutter covers in either. My rack went on in about 2 hours from start to finish but I credit that to a few videos I have seen in the past and then reading the instructions a few times and ensuring I laid out the parts on the carpet before I started. I found out as well that I needed the factory gutter channel and then after I put the FR rail up there I decided I don't want to need to mess with them because of all the crap I found under the factory rails when I took them off.
My opinion is, the factory rails do not drain with all that crap up there so I left it off an I have no drainage or rubbish hanging out after off-road trips. Wet leaves, sticks, mud and all of that stuff under the factory rails is what will lead to rust. Additionally, if you ********** the FR rack on something, I want to see the roof mounts anytime to verify I didn't break anything. I have looked at using home door threshold seals that fit in there perfectly. Punch a hole where the mounts are and you can use one piece the length of the roof on each side for about $30. Not a chance I'm buying the $150 factory gutter covers to cut them up again...hahaha
When I installed the rack, I left everything very snug but loose enough to move around a bit before final tightening. Once I had my alignment correct, I tightened down the rails and then pulled the rack off for final torque, put it back up and it fit perfectly.
I have the wind deflector on and put it on after I forgot about it once it was on the truck for alignment. When it came off for final torqueing, I then installed the wind deflector. I think it helps with noise personally but now that I have my awning on the side, noise is noise and who knows what if anything it is doing now. I plan to run 2 x 20" or 2 x 10" lights up there in front eventually and make my own wind deflector/air damn that bumps up against the roof line and the rack...more for roof protection than anything and maybe help with some noise but I will flip it up when on the trail and need the lights. Too be honest, as big as the rack is, its pretty damn quiet IMO and I love it's capabilities. Awning and RTT install on this rack with my Pelican Cases on the roof are simple and I have all the faith in the world in FR products. The best part is, I roughed it up a few times on the trails and the scratches are there but never gonna rust.
Also, before I installed the black hardware caps, I put a drop of black gasket sealer in there and slipped the caps on so water does not penetrate. Did the same at the reinforcing rails anywhere there is a gap and under the mount bolts from the rack to the roof.
Lastly, I think my FR rack shipping and packaging to Hawaii was the best of ANY product I have ever seen. I could not have been more happy with the product and services of FR thus far. Just my two cents.