I am guessing you have the 2.4 duratorq engine in this and you have replaced the dual mass flywheel and clutch,you could remove the fan belt and see if that helps your knock then you know it is one of the pulleys giving you problems,another thing to look for is the crankshaft pulley which causes a similar rumble/knock to a flywheel problem,these are rubber mounted and break up through time,worth a look good luck.
cdc
August 2011