Just to clarify, I believe that the distinction of the 16" rims being only for the Tacomas is due to the fact that all 5th gen 4runners require 17" rims, and they're not including us guys with the old sr5 4th gens. I would be really confident that those 16" TRD pros would be fine for you.
I have the black TRD pro 17" rims on my '05. The offset is +4mm and allows my 33" tires to clear my JBA UCAs. They work really well and look nice too.
The stock brakes on the sr5 4th gens are small enough to allow the use of a 16" wheel. However, the sport edition and Limited brakes are larger...
I know that you mentioned that the problem most likely isn't rain, but when I bought my truck, it had a similar problem. I found that the cause was that the cowl at the base of the windshield wasn't fully seated. On the underside of the cowl is a lip that diverts water away from the opening...
