not sure about the size of that replacement stud, but maybe you could cut a sleeve of small tube, like a thick wall washer, to fill the gap if the shoulder is wide enuff to hold
if ya wanna see the works inside the door, the assembly manual isn't bad, just hafta study it for awhile
the putty I use a lot is the common one used by electricians called Duct Seal - cheap, comes in a block, never gets real hard, quite like the original stuff - be a pound or 2 in daBus

Bill