Wow that sounds proper bad. Sounds like a clutch/clutch release bearing. Just because the clutch is new, doesn't mean it can't be faulty. If the clutch is faulty it can cause engine to run rough with high revs. Misfiring could be related but could well be a separate issue. I know the coil packs are prone to fault and disconnecting each one like you did for change, doesn't always mean they are not faulty. I would concentrate on the knocking first, that ain't good and could blow apart at any time. Get the gearbox off and see what's happening asap.
Si