First off, I would like to thank everyone for their input with regard to this matter. I appreciate it very much. The drain holes/exits are located on the underside of the rocker panels. The area where the metal flange is, to be precise. There are a certain number of "openings" on the driver's side on my particular truck) and a certain number on the passenger side. I cannot recall the numbers as of this posting. If you remove the sill plate trim panel on the inside of the truck you will (with some difficulty) be able to see the inside of the rocker. If the drains are clear you should be able to see daylight coming in from underneath. I was not able to. A small wire, inserted through the flange opening and then moved back and forth (don't be too gentle) opened up the exits. The opening from the outside as you look at it is just a very small indent in the metal. It's very easy to miss if you're not looking for it. Anyway, once I had the openings clear, a shoppe vac application, and then a garden hose through one of the topside openings did the trick. Make sure you've got water flowing easily through ALL the openings before you close everything back up. Again, thank you to everyone for their respective input on this matter. Now, on to ANOTHER problem...

 

So I've battled water coming in from the sunroof area as well, although my problem seemed to be clogged drains. When searching the forums I couldn't find any clear answers as to the locations of the drain hoses. On the last go around I was successful with simply opening the sunroof and flushing the drains with water. There is one at each corner, the two in the front are very easy to see from the top but the two in the back you can't see.
Anyway, I am parting out this 2nd gen and once I got the headliner off I could see the whole story a bit better, so I thought I would take some pics & share.

Here is a shot of the sun roof assy with the headliner removed.

This is the left rear drain - notice the hose gets a little pinched here.

This is the end of the drain hose pulled out from behind the left rear quarter area. Note that it does not go all the way to the bottom of the truck.

Here is the right front drain hose.

Here is where the right front drain hose ends behind the lower kick panel area.

 

Wow! I've been trying to get a visual, via the internet, for days to see if someone actually broke everything down to fix clogged drain hoses for the sunroof. You've got the best breakdown there is. Thanks so much for taking the photos.

My issue is driver side rear drain hole. Can you provide your best recommendations/tips to pull back the plastic panels and headliner in order to clear it? I'm dreading pulling back the headliner as I'm afraid I won't get it back in place properly when finished. I'm thinking, based on your photos, I'll just unclip the tube from the sunroof and run some weed eater line through it make sure it's clear. Then run water through to test. Also, clear any debris, possibly, in the sunroof valley.

Your assistance is greatly appreciated.

 

wow, that first post was very confusing.

don't remove the headliner at all. Take off the trim panels where the drain hoses go, then blow compressed air through the hose from the open end. There...clean.

Then extend the hose so its drains directly out of the cab. no sense having water build up in your rockers.

 

tip for clearing sunroof drain holes = run a length of weed wacker line through the hose. it's rigid yet flexible enough to do the job and clear it out quickly. follow up with air compressor if you like.

 

Thanks for your help. To be more specific, do you have any tips on how to take down the panels? It looks like I would need to undo the seatbelt bolt at top and also the panel holding the carpet down that runs along the the back door/gate. And then pop off the large driver's side panel.

I haven't begun the project as I didn't want to make a mess or crack something that doesn't need to be removed to access the rear drainage tubes.
Thanks again.