This 100%!! Part of the complaints were about noise. Every after market part is louder and squeaks than the stock part. Every one rattles more and makes more noise. Ford put millions of dollars and decades of time into researching how to keep things quiet, dollars that no after market company in the world could spend. On top of that, as
@Truckasaurus was getting at, bypass shocks mechanically make significantly more noise.
Rebuild the stock Fox. Ability to be rebuilt is what gives the Raptor's shocks such a leg up over any other vehicle on the market. Sure better dampening...blah blah, but when they get trashed, just rebuilding such a performant shock is so much cheaper than replacing. Also, replace bushing, oil contact spot, etc. etc. A lot of places do swaps these days, so you can have fresh shocks instantly for a little more than the rebuild price.
I have Fiberwerks +2/+2 on a Gen1, using the stock liners, and still have rubbing with my 37" Grabbers. Just minor rubbing on the fender liner when at full compression or full lock (I try never to have both of those happen at the same time). Just saying, don't automatically assume new fenders will fix it.
Why upgrade breaks? Mostly rhetorical. I just mean that I would spend >$20k on my truck before I upgraded breaks. Steel lines, upgraded pads, absolutely, but new rotors and calipers, not for a while. Generally speaking, upgraded breaks provide better repeat/continuous use without fading; they provide minimal benefits to stopping distance in a day-to-day driving situation. Off-road, I run pretty much on the gas until I need to be on the breaks and I've never had significant fade from the stock. I love red calipers and slotted/drilled rotors as much as the next guy, but budget wise I couldn't do breaks in the first $10k on the truck.
My recommendation, as someone else here mentioned already, is to tackle one issue at a time and really research each piece. A full/big build thread is a little chaotic to request recommendations or solicit feedback. They are great for showing off, which I fully support and love reading through, but not great for solving issues. Personally, I would rather rank my issues in order that I want them fixed, then find the best solution for each one, in that order, until my budget is used up; as opposed to starting with a budget and trying to cram everything into it.