I am not sure what you mean by chugging at idle,do you mean an engine knock/rattle?Have seen g/box first motion shaft/bearing damage if DMF are allowed to rattle for an extended period and the fact the noise disappears when clutch is depressed points to your DMF again,I take it all your engine g/box mounts are ok and all bolts tightened after the g/box removal,it is very difficult to determine if your g/box has to be removed again without hearing/seeing the fault at hand.If it just happened when engine is cold then it may be worth checking your heater plugs for operation which can cause an engine/diesel knock due to unburnt fuel problems but wish you the best of luck.
cdc
September 2013