i am certain any clunking or squeaking or squeaking or other noises you’re worried about have nothing to do with the chain alignment!
Just an update. Maybe not the proper place for the fix but you were right with this noise concern. As mentioned above, the noise started with a clicking/rattling/knocking noise while climbing a steep grade. You would almost think that it was related to the rotation of the pedals since the noise frequency would follow the pedal rotation. After time, the noise concern happened while going over bumps in the road also. You would hear this same noise while going over every crack in the road and sometimes it could be constantly. Although the pedal noise and bump noise sounded alike I wasn't certain at the time it was the same or related to the same concern.
The noise concern occurred from the time the bike was new till presently when I found the concern and verified it with a long for me ride (34 miles, yesterday). Like mentioned previously, it was in the shop 3 times and various emails to Rider Care with no repairs that fixed the noise concern. The second time in to address the noise, "more time" was spent trying to convince me that the noise they didn't hear was normal then looking for the noise. The third time (after replacing the cassette) I rode the bike in the parking lot and the noise was always there. An employee took a ride in the parking lot to verify. They indicated that they didn't have time to look at it so I just took it. Yes, although they appeared to be not interested in repairing this, I really didn't want them to touch my bike anymore. They already put 2 small scratches in the top tube when they removed the TCU and just let it hang there while rubbing it against the frame. Every time I took the bike in I would remove every item off the bike that didn't come the way the bike did. Including installing the original pedals. I didn't want blame to be put on those items.
Ok, the cause. It was the steering bezel (duckbill) rubbing on the frame. There were very slight rubbing marks on the top tube under the bezel on the left side. I never thought anything about it at first but I was getting desperate looking at various posts on this forum and torquing all the bolts. I kinda remember seeing something about this on this forum but I can't find it at this time. I don't know if this is the proper repair but I sanded the bottom of the bezel to give it more clearance. I also checked the fork for any excessive play but I don't see any play in the fork. Presently, I don't want to mess with the adjustment of the headset. It is always easy to make a story fit after finding the solution but if you think about it, it makes sense. The fork movement when it was stressed pushed the bezel into the top tube creating the noise. Would/could this happen with an alloy frame or is this only with carbon frames since noise carries differently?
It was a relief to find this noise. For over 90 days, riding my bike turned out to be looking for the noise instead of enjoying the ride. Ok, I admit, although the noiseless ride was enjoyable at first, I was getting tired at the end. Maybe, because there was no noise to aggravate me. About the shop, there are good people there. They are pleasant to talk to and very friendly. I know the technician is always busy. So maybe, hiring another technician would be the solution. By the way, this is a Specialized owned store. As far as Rider Care, they want you to take it back to the store.
Thank you to everyone sharing your time.