Ok... Just had a look at a manual clutch pedal assembly, I stripped out the barrel and took a good look at the hole it slots into on the pedal arm itself and the plunger.
It is indeed worn ever so slightly oval, not enough to cause the clunking you are experiencing. I had a smaller barrel pin handy from another type of car that I tried in as an experiment and indeed, it started clunking like hell on clutch release and depression. I can only assume that if the hole has elongated or even worn larger then even with a new correct size barrel pin, it will still clunk despite minescule movement, it magnifies due to the fulcrum effect the pedal assembly offers.
I would also take out the new pin and inspect for it for tell tale bright marks that will correlate to where it is tight and where it is loose if indeed, any play is there at the pedal link.
It's a shame the lube didn't come with a straw, if you can "jerry rig" one to the end then you can lift up the rubber dust seal between the plunger arm with a small screwdriver and then insert the straw directly into the bore to give it a damn good spray and see if that alleviates the issue... Clean off the excess thoroughly for safety sake, use IPA or brake cleaner to dissolve any over spill/spray from the area.
I wouldn't advise just spraying chain grease over all the mechanism randomly though. All it takes is just a few stray drops to come down later while you are driving along to land on the pedal rubbers and your foot slip off the clutch pedal and hit the brake instead and before you know it, rear ended
Try that first but contact someone like AutoLusso or RGWM etc. about the price of a good, used clutch pedal, just in case mate