1. Sounds like an issue with the indexing
I redid the FD after the bike shop installed the chainstay (CSD) bracket upside down & I was able to get the front to shift in 2 clicks
Because of all the futzing around in the front the chain line may not be perfect which is probably throwing off the rear indexing
2. Where does the chain rub? On the FD? Then it's an FD setup issue. Set the inner limit screw. If the chain rubs in the big/big gear combination, then that's a reminder from your bike to shift to the small ring
Yes. Chain rubs against inner part of the FD, when in big/big & thats the only time it does that
3. Sounds weird and could be any number of things. Does it only happen when pedalling? Are your QR skewers properly tightened? Does your tire rub on the chainstay? Do your brake pads rub when yanking on the bike during pedalling while standing? I did have noise coming from brand new Ultra Torque cups on more than one occasion, because the brand new rubber seals make a noise when the crank spindle is rubbing against them. It would usually disappear after a few rides. But that usually sounded like a very high pitched squeaking.
Tires are not rubbing & I will check the skewers (thanks for adding that). I did switch the grubs from small black alloy steel to the original stainless steel in the front handlebar so that may have caused the issue
4. Sounds like something coming from any of the interfaces on the front. Check the handlebar grub screws. Are they still torqued correctly? Do you have headset play? Also, I think what @jr223 actually meant, is if you greased the headset bearings when you pressed them into the frame's headtube. Those could creak as well.
Zero headset play. Yes every single thing was lubed with PPL-1 or HPG-1 from ParkTool.
I will recheck all screws. Because the saddle fell off on my 1st ride & I had to buy a brand new titanium bolt, I am extremely apprehensive about getting on the bike in case the tech sabotaged it since it's a chinese frame
(Yes, I'm probably being paranoid here, but I had zero creaks before I dropped the bike off & I'm very sure the saddle was torqued correctly by me)