The sunroofs are different; the mounting bolts are the problem.
The sunroof drain is a design failure; the only one I can point to on the entire truck. There are too many design points which all have to be within spec, or the system fails. Spectacularly.
There a a couple of points to look at, if you have a couple of weeks to chase them down. It takes this long, because you have to flood the sunroof drains to verify that you've found the root cause, and that takes time. Here goes:
1. The entire sunroof drain system is designed to channel water into the drains, not to exclude it from the sunroof using a waterproof seal. Toyota evidently looked at the problem and took a statistical approach to the solution. Even a 100% waterproof seal will eventually leak, so why not deal with the leak in the design? I can't say I disagree with the approach, but the execution is, well, I won't share those thoughts.
2. The glass gasket (seal) is supposed to restrict the volume of water which can flow into the drain system, so that it's never more than the downtubes can discharge. The problem here is that the drains are gravity fed, and the tubes have air in them. This means that any time the column of air reaches a sufficient length to approximate the ambient air pressure, the system will not drain and the downtubes will fill. This is why the sunroof leaks.
3. There are two design features which "help" to ensure that the seal excludes the ingress of water so that the air columns can't support the water:
a) there is a thin solid rubber strip at each corner (sorry, I don't have photos at the moment, but I'll post them later) which is intended to force the glass gasket to expand when the sunroof is closed. This strip has to be there or the seal will fail.
b) as
@gummycarbs mentioned, there are plastic corner trim pieces, only at the front corners of the sunroof pan, which are supposed to act as dams to channel the water into the drain inlets. The later designs included a lip to help this happen. This was a design bandaid from Mr. T and it didn't address the root cause (I'm getting to that).
4. The downtubes can slip off the nipples at the sunroof pan, most likely due to overenthusiastic cleaning with either compressed air or a snake. The only way to see if this is your problem is to drop the headliner. This can happen to either the front or rear.
5. The lower ends of the (front) downtubes are routed into the pockets in the kickpanels. This is where the root cause of the system failure lies. The discharge points (drains) are actually not in these pockets, but are in the rocker panels, which are separate sheetmetal body parts. In order for the water from the downtubes to get into the rocker panels to exit via the discharge points, this kickpanel pocket has to fill up and overflow into the rocker panels.
6. There are four or five (can't remember which) small plugs in the lower surface (horizontal, not vertical, those big ones are cleanouts) which can be removed to drain any excess water from the rocker panels which hasn't found its way out.
Some owners remove the plugs when the drains (which are formed by a crease in the inner sheetmetal before the inner and outer panels are glued together) become clogged. IMHO, this only makes a bad situation worse.
The problem is not only that the kickpanel pocket has to fill up (by the way, have you noticed how much wiring is in there?) and overflow in the rocker panel, but any dirt that gets into the footwells will find its way into the rocker panel void and plug the sunroof drains. There is no way to clean the rocker panel drain area effectively. Yes, you can run a bottle brush in there, but you can't clean it all and you'll remove some paint which will leave an unpainted sheetmetal panel open to constant water exposure. Not a good plan, IMHO.
The only practical solution, not mine but I agree with it 100%, is to remove one of the two sheetmetal screws (the rearmost one, you don't need both of them) inside the pocket and route the drain downtubes into the hole. This guarantees that any water which gets into the downtube will drain out. No air column can form in this modification and the hole can be sealed around the exit point of the tube. Further, this mod ensures that the rocker panels can't rust out, since there's never any water in them.
I'm working on this mod on one of mine now and will post the write up with photos soon. It's under cover in the dry garage until I'm finished.
