GOOGLE NEXUS 7 AUTO UPDATE TO V188.8.131.52 AVAILABLE!
ToolKit v3.5.0 (16th Oct 2012)
+Updated TWRP Recovery to V184.108.40.206
+Edited drivers text for better wording
+Changed Download link for 4.1.2 to google site to fix original corrupted image file
+Checked the root routines and changed some timings to make things run more smoothly
+Fixed some minor text errors
I have checked and verified that the root/busybox procedure works for both Android 4.1.2 OTA and Stock Rom flash from google. I also had no problem with the 4.41 bootloader and custom recoverys so if people are having trouble I would suggest a reflash of the Stock Rom.