If the TOD off switched is installed correctly, there is no reason why it would cause any issues. Seems like the problem arose when you put the T-case in 4lo. The big clunk was probably the drive shaft if you haven't greased the zerks recently. Do you have manual hubs? You need them to properly disconnect the 4wd with a TOD off switch.
(if you have manual hubs) I would start by pulling the pigtail on the TOD ECU. That will ensure its not transferring power to the front and you can see if the issue continues.