what the other guy posted above, and makes sense that a really trashed motor mount could clunk on start up and stop. I would get underneath there with a really long screwdriver or extention or whatever, and put it to the motor mounts, one at a time and see if that's the spot. You might be able to hear it without the device to your ear. If it's coming from the bell housing, should be obvious with something to your ear, then it's likely the TC bolts.
If it's TC bolts: Since they have been known to come loose on these. I would pull the starter, and then pull the access cover above where the starter was, and remove the 4 TC bolts one at a time and replace them to spec with red locktite. If they are loose, you found your clunk, if not, on to the next thing.
_________________ 05 CRD: H.D.S2 stat,WW Ironrock trilink&LCA's, OX rear,ARB front, 4.10's, ARB bumper, Suncoast,OME 3.5, JBA UCA,rock rails, Moabs&265/75 Duratracs, GDE tunes ,FFD fan,ARP's, 2 micron fuel, new valves,sasquatch battery tray & grid heater, tensioner relocated Mech fan, VH & AC delete
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