Push in the clutch pedal and see if it changes . Put it in gear and slowly release the pedal and see what the sound does.
You said you surfaced the flywheel. If it is OEM it has the dual mass flywheel. You may have a flywheel about to come apart. ZF doc told me the early flywheels had no cover over the seal in the flywheel crap can get in and take out the seal.Then things start to go wrong.
If it appears to be flywheel related you might want to contact him, he is very good about sharing information.
Scav.
BTW Before I replaced my clutch and flywheel I had a similar rhythm but more of a click when it was warmed up. That is gone. Did you notice a click before the knock started ?
I located this after I posted.
ZF dual mass flywheel