Brake judder may not necessarily be from overtorquing...read through the literature on the Stoptech website. They make the "Big Brake Kit" for the 1st-gen Tundras, and have a wealth of technical whitepapers, including one regarding "warped rotors". There are a few different causes for that awkward symptom.
I have only ever seen one warped rotor in the four sets of rotors which have been on my truck (OEM front, aftermarket front, one warped in first rear pair, new rear pair). It was likely a factory casting or machining defect...the second set in the rear was slightly out of true as well, but they were machined true before they were ever on the truck.
Anyhoo...I always use a torque wrench, like Rich said for everything except the skid plate bolts.
If you don't have a torque spec, see if you can locate a specification for the weakest threaded metal.
What that means is, if you're running a Grade 8 bolt (or 10.something, if metric...10.8 or 10.9, I forget) in to an aluminum head, use the torque spec for that thread diameter and pitch for aluminum. Same goes for replacement bolts in critical locations...you can get Bowmalloy bolts for your bumpers and receiver, but you'll still be torque-limited by the softer side of the fastener.
Now, if you have replaced the nut as well as the bolt (as some of us have done with skid plates and bumpers), then look up the torque spec for that size, pitch and grade, and use at least the minimum specification.
You may find in some cases where you've made a significant upgrade that it's just not reasonable for you to put finish torque on the fastener...some of those fasteners can take over 200ft-lb torque. When in that situation, I set the wrench to what I can reasonably achieve with a 2.5' 1/2" drive torque wrench and a 3' breaker bar.
Sometimes it's awfully difficult to reach a fastener, like Kovawa mentioned. Extensions and even u-joints won't change the torque,
but just like your driveshaft carrier bearing, the joint and/or extension
must be supported or you'll lose torque as the extension or joint flexes over. It's almost impossible on large fasteners, but works great on spark plugs...particularly the ones at the back of the engine, if you have ABS.
Also keep in mind a "crow's foot" wrench will change the amount of torque you're applying. The wrench will break at the same torque, but that torque will not be reflected at the fastener if the business end of your tool is offset from the head of the wrench. There's usually a different specification for a crow's foot, for example with the fuel line connector at the rear of the block...or is it the pulse damper? Whichever. If you're swapping your starter you'll find it
. There's a direct torque, and an SST (Special Service Tool) torque, the SST is basically a crow's foot on a torque wrench.
-Sean