The only actual adjustment on the Tundras, or any Toyota for that matter, is in the door striker. The hinge bolts are "shoulder bolts" which fill the hinge holes completely, thus, no adjustment. If you need to bring the door in at the top, get the window down, put your knee against a solid area inside the door, and pull it in at the top. Its not easy but is effective. Another method is get a short 2x4 and place it at the bottom of the door between the rocker. Make sure you get it at the thick part of the door, not just the lip, then push in at the top of the door. I know it doesnt sound technical, but if there is no adjustment from the factory, you have to "bend to fit". These are basically cures for wind noise or water leaks. You can also loosen the door striker slightly and tap it in a bit, then re-tighten it, which will bring the door in and help with any rattles caused by a loose fit problem. Be careful though, those striker bolts are in with lock-tite and are pretty tight. These are the only adjustments to the doors and is about all the dealer or anyone else can do. How do I know? I worked as a bodyman for Ford/Toyota dealership for over 15 years.
$125 would be wasted money for something you could try yourself. They would just give it to some kid to do exactly what I described. Even then, there would be no guarantees. Honestly, about the only things that will get Toyotas out of adjustment, is either a prior accident or wore out hinges, which you can tell by moving the door up and down from the rear. Good luck with it.