I work part time at an auto shop.  And we always hand torque the
lug nuts with a torque wrench.  I've even warped the rotors on my 89
toyota truck by hand tightening them with my toyota supplied lug wrench
and I tried to tighten them evenly.  So be sure to hand torque them, to
about 80 to 90 ftlbs on steel wheels.  When you cut them to try and
save them the metal is thinner so will heat up faster.  I just replace
rotors after they warp.  And I use the cheap chinese generic rotors and
never had a problem with them if I torque them.

You might check the TSBs here and see if any apply.
http://www.alldata.com/TSB/60/006027AD.html

There is a TSB to install the 2003 larger calipers, but Toyota only pays
if you are within the 3-yr/36 month warranty period.  They might pay for
good customers after the warranty has expired.  This is a big job.  New
wheels bearings are needed because the old ones are pulled to install
new backing plates for the new calipers.  Figure something like $1200.
This is not at item for which a so-called extended warranty will pay
('cuz they aren't warranties; they're pre-paid repair contracts).

Two possibilities...get the next brake job done at a Toyota dealership
and have them replace and replace the warped parts under their 1-yr
service warranty until Toyota Motor Corp. agrees to pay for the TSB.
Or, buy premium rotors and premium pads.  I like Porterfield,
Performance Friction, and Hawk pads.  It also is very possible that the
rotors are not warping.  The brake judder you feel could be caused by
other things...brake pad depositions on the rotor surface are one cause.
 http://www.stoptech.com/whitepapers/warped_rotors_myth.htm

Ken