My recommendation to you is to first identify the source of the leak - in your case it may or may not be from the third brake light. There are some other simpler fixes - for example the drain holes on the bottom of the tailgate may be clogged, your weatherstrip might be compromised or not on right, etc. You can do the water test - i.e. ideally remove the trim on the back door, leave a hose on the roof draining to the back of the truck, and sit inside and watch for water collection....Great write up! Looking back on it, is it necessary to remove anything on the inside of the hatch? Looks like the fix can all be done on the outside part of the hatch (ie, just focusing cleaning and re-sealing the brake light area).
Just got a 99 back in May (long time lurker) with 85K on it (has the the rear locker). Love it, but my right rear cargo area does have a tendency to get wet, need to try and fix it at some point.