C30 clicking noise when changing gear

[Tokominovo]

Hi everyone - this is my first time posting.
I have a C30 2012 D2 with around 55000 miles on the clock. I recently had to get my “inner” CV boots changed since they were really badly worn - outer ones weren’t too bad. I ended up getting them all replaced along with new drop links at the front as well since it was mentioned that this might have been what was causing the inner boots to fail. One of the drive shafts (driver side I think) was also replaced but with a second hand part since the original one collapsed during removal. The gear box oil was replaced too. Since all of this, I’ve noticed this subtle but concerning clicking noise when changing gear mostly when coming out of 3rd and going into 4th and sometimes when taking up the drive. There is no whining or noise when rolling along or turning so I doubt it’s the outer CV joint. The clutch sometimes whines when I’m moving off in first but disappears when i sink the pedal or give it a bit more gas (pilot/throw out bearing maybe?) but I don’t think it’s connected as it’s been there before this clicking noise. It has been suggested it could be a bad transmission or engine mount?? Any ideas? Thank you in advance.