Maybe it's placebo, but I feel like my clunking is getting worse. For everyone that's having the issue of clunking
after shifting (not during) when you're letting off the clutch and giving it gas at low speeds, what year model do you have. Seems most common for 2016s from what I've been reading, but it could be just that no one else has posted their model year. I have a Sept 2015 built 2016. This is really the only car I drive, but I don't remember any clunking like this on my old car which was also a Ford front wheel drive manual. It's annoying at best, but it seems like there's some major slop somewhere there shouldn't be and it's gotta be in either the CV axles, motor mounts, or transmission. I have a Cobb RMM and I torqued the bolts to spec. I have been under it a couple times since and checked the bolts on the RMM and they are fine. I checked the bolts on the other two mounts and they are good as far as I can tell.
Here's a video I found that shows it's not a shifter issue. It's when you add gas and it picks up the slack somewhere and clunks.
https://www.youtube.com/watch?v=xZViiG1Y7Xo