The condensate drain on models with rear a/c should be a little rubber thing going through the passenger floor and exiting roughly above the exhaust pipe.
GM issued a TSB with revised weatherstripping that supposedly addressed some of the problems. I can confirm that the tailgate weatherstripping sold by LMC has the foam insulator and appears identical to the GM version revised under the TSB. It didn't help my issue, but maybe it will be of some use:
http://www.revbase.com/BBBMotor/TSb/DownloadPdf?id=1589
The alignment marks referred to in the TSB are small dabs of paint applied to the weatherstripping.
Do you have the tailgate or cargo doors? The tailgate on my 98 two-door doesn't meet the bottom of the liftglass. There's a gap and no amount of adjustment will close it. New weatherstripping did not help.
These photos are not of my truck, but show the exact same issue. The exterior side trim panels have been removed to better show the gap:
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