Sounds like you didn't use the jig remedy but pulled the cover to fix the pin problem. If a guy uses the jig, drill, tap,plug solution, how does he know the pin is in the hole when he does the job? The pin could already be in the bottom of the gearcase, right? Just thought I'd ask, since you have probably mulled all this over. I have a '96 with a virgin dowl pin, and am preparing to go after it.
'96 2500,354gears,PAC brake,4" exhaust,reworked AT and high miles