Check to see if the bolts are all tight, there is four 14 mm bolts underneath, aside from that without seeing it is hard to figure out. I would say to bring it to the dealer and see if it may be a warranty issue, I LOVE warranty.
I too had the same problem with my 02 taco.
I am a body repair tech at a high end collision repair shop.
I found that the hood fit a little loose at the rear (wiper side). to fix you will need to open hood, grab the back edge of the hood(while reaching over motor compartment) with one hand. place other hand on front edge of hood near the support rod. Now GENTLY but very firm pull bottom of hood towards you. ( Dont be a dummie here and bend your hood in half). You want to SLIGHTLY bow the back edge of the hood.
I hope this helps everybody.
Mark, if you pull the hood underneath like that it will make the back edge of your hood lower than the top of your fenders. You can't lower the back of your fenders. I think this is not something that someone outside of bodyshop should try, the hood mount area is high strength steel. Another possible solution is to see if you can put some shims underneath the plastic cowl to give a tighter seal to the hood rubber, no possible hood bending or sheet metat fitment problems.
you only want to pull the center. The bow should be so slight it will not change the fender lines. The shims may work for you too. All the bend does is make the back edge fit tighter to the weatherstrip.
I don't beleive that the hinges would be a problem, I also work in a high end collision center, which mainly serves Toyotas, and chevs. In my experience there has been very little problem with Toyota hinges. Toyota has very good quality as far as auto manufacturers go. Mark's hood adjustment should also work but I would be very cautious with this because it would be easy to put a kink into the hood this way.