[Eee Pad Transformer Q&A, Help & Troubleshooting] toupeiro:
Here's the basis of the script.

#!/bin/bash

BACKUP_DIR="tf101-backup-`date +%Y%m%d%H%M%S`"
mkdir $BACKUP_DIR

clear
echo -e "\nAsus Transformer TF101 Universal Root"
echo -e "==================================================="
echo -e "Disconnect your tablet from usb (if connected) and turn it off (if it's not)."
echo -e "Press and hold the UP Volume and the power button for ~5sec."
echo -e "For now the tablet screen should stay off, it's perfectly normal"
echo -e "Now connect to usb"
read -p "Press any key when you're ready."

cd root
./nvflash --bct transformer.bct --setbct --configfile flash.cfg --bl bootloader.bin --odmdata 0x300d8011 --sbk 0x1682CCD8 0x8A1A43EA 0xA532EEB6 0xECFE1D98 --sync

echo -e "\nMaking a backup of your boot and recovery partitions in $BACKUP_DIR... \n"
./nvflash --resume --read 6 ../$BACKUP_DIR/boot.img
./nvflash --resume --read 5 ../$BACKUP_DIR/recovery.img

if [ -f ../$BACKUP_DIR/boot.img ] && [ -f ../$BACKUP_DIR/recovery.img ]; then
cp ../$BACKUP_DIR/boot.img ./
cp ../$BACKUP_DIR/recovery.img ./
chmod +x insecure.sh
./insecure.sh boot.img
else
echo -e "\n!!ERROR!!: Unable to read boot and/or recovery image from your tablet\n\n"
read -p "Press any key to exit"
exit 1
fi

if [ -f my_boot.img ]; then
echo -e "\nWrite back the modified boot partition... \n"
./nvflash --resume --download 6 my_boot.img
else
echo -e "\nThere were some ERRORS creating boot image\n"
echo -e "\nThe script will now exit\n"
echo -e "\n\tYour tablet is NOT rooted.\n"
read -p "Press any key to exit"
exit 1
fi

clear
while true; do
echo -e "ClockWorkMod (CWM)"
echo -e "====================================="
echo -e "ClockWorkMod recovery is a recovery image that let's you do some funny things like make a nandroid backup, installing custom rom and much more"
echo -e "This is not necessary for root\n"
echo -e "NOTE: if you install CWM you won't be able to update your tablet with the OTA firmware from ASUS, until you revert back to the stock recovery\n"
read -p "Do you wish to install clockworkmod recovery? [y/N]" yn
if [ ! "$yn" ]; then
yn="n"
fi
case $yn in
[Yy]* ) chmod +x recovery.sh ; ./recovery.sh recovery.img ; break;;
[Nn]* ) break;;
* ) clear ; echo -e "Please answer yes or no.\n";;
esac
done

if [ -f my_recovery.img ]; then
echo -e "\nWrite back the modified recovery partition... \n"
./nvflash --resume --download 5 my_recovery.img
fi

clear
echo -e "\nNow press and hold the power button for ~10sec."
echo -e "\nYour tablet should reboot. When android is fully loaded, go to Settings -> Applications -> Development and make sure USB Debugging is enabled."
read -p "Press any key when you're ready."

./adb remount
./adb push su /system/xbin/su
./adb shell chmod 6755 /system/xbin/su
./adb push Superuser.apk /system/app/Superuser.apk
./adb reboot

rm -f my_boot.img
rm -f my_recovery.img

cd ..
clear
echo -e "Done.\nYour tablet is now rooted.\n\nEnjoy!.\n"

Now, the one thing I noticed I needed to do after the flash was update the version of superuser.apk and su that the universal installer comes with. I got those new versions here:

EDIT: I can't post outside links yet so you'll have to decipher it. :) http colon whack/whack/ androidsu dot com whack/ superuser whack/

then placed them in the relavent locations so the script would push them up. I also didn't do CWM. personal choice.