2020 ST Various Issues - Exhaust / Drivetrain Vibration / Suspension Clunk

This is my first post here, so hello all! I'm a used-to-be gearhead poking my head in the gearhead void again for the first time in a while. I have a tendency to go deep on modding cars once I start, so trying to dip a toe in could be difficult

I've owned my 2020 ST since July of this year. Bought it at about 62K from a dealer my neighbor worked at for many years and I've always had a good working relationship with him/the dealer he worked at and my Fords. He would swap vehicles with me and take it into the dealer for service, whatever. Well, I knew about the possible ST issues before I purchased the vehicle and decided my awesome neighbor would be able to help me work through whatever might arise. Fast forward to about August and my neighbor quit the dealership and is thinking about retiring. This is also about the time that I'd gotten to know my vehicle well enough to know what is an issue on it (and also some issues started getting worse). All these things are still an issue.

I work the opposite direction of the dealership that I bought it from and so I decided to try a new dealership to see how they would treat me. I've got the Ford Gold CPO warranty on the vehicle, so I would obviously like to get as many repairs covered under warranty as possible.

These were my complaints and their responses:

• Suspension Clunk in front end, especially on gravel roads or quite rough terrain (I said this seemed like a strut mount to me)
  • They came back with telling me that there is a tie rod end that needs to be replaced. This may be the case but I don't think that it is the cause of my clunk
• Drivetrain vibration - comes and goes, can feel it in the seats and center console. Sometimes, when cruising at higher speeds, like 45-65ish mph, you can hear it more than feel it, there is a low, bass-like, rumble.
  • They said that my front CV boot is ripped. This is true, I'm sure, but the vibrations are not felt through the steering wheel, so I doubt this is the source of my issue.
• Exhaust leak - I went under the vehicle and can verify that the cats are cracked at the welds but also the pipe on the drivers side cat is cracked about halfway from the bottom of the cat to the mid-pipes
  • They confirmed this, but they also told me that my mid pipes (which definitely have the usual rattle) are going to be destroyed when they replace my cats. They stated that while my cats were covered under warranty the mid pipe (which were in need of replacement anyhow) are NOT covered under my warranty and between parts and labor the total for those will be something like just north of $700. I said to them that at that price I would opt to just put an aftermarket exhaust on it and then take it in for the catalytic replacement. They told me that Ford would not honor the warranty on the cats if I did this. That would NOT seem correct to me, especially since you saw that the cats were damaged with a fully stock vehicle.
• Transmission whine and shifting issues. There is a moderate to huge amount of "supercharger" whine that occurs during acceleration and between shifts. It's embarrassing, to be honest. Also, sometimes the shifts are jerky due to delay, and sometimes the shifts are quick and harsh. In addition, in certain situations, for example, when accelerating moderately hard in 4th gear, you can feel slippage in the transmission before it ultimately grabs and goes.
  • They didn't tell me anything other than there is a TSB on the issue and they must follow the protocol in order to eventually resolve the issue fully (I'm thinking this will eventually conclude in a full transmission replacement). The first step that they took, I believe, is to reset the transmission strategy. When I picked up the vehicle, I was actually in shock. It worked, the transmission was quieter (not completely normal, I would say, but much improved), seemed to not have the slippage and generally shifted better. The problem, as you guessed it, I'm sure, is that as the transmission re-learned, it got worse again, and it's back to the same place (if not worse) as it originally was.

So, that is a lot, but I'm wondering the following:

• Does the mid pipe portion of what the dealership is saying make sense? Does this seem reasonable? I feel like if a failed warrantied part being replaced causes a non warrantied part to fail, that non warrantied part should be covered as well. Otherwise, I feel like I should be able to replace it with a non OEM part since it is not a part of the warranty claim anyhow.
• Regarding the transmission issues, is there any way to expedite this process? I really want to start modding the ST but I'm not willing to pay out of pocket for a transmission replacement when the transmission was messed up to begin with. If I were to burn up a transmission because of mods, that is one thing, but this is a faulty unit, clearly.
• The JXB Support bearing upgrade - has anyone gotten positive results from this change? I feel like it is the driveshaft that is causing this vibration, and I feel like this could fix or help the issue immensely, but I have concerns about possibly making it worse too?

I'm just feeling stuck at this crossroads and I don't know how to get the best results.

FWIW, I like the ST, it can be a great family hauler while still being sporty and fun while having enough luxury to keep me happy!