Okay, the shop did not replace all of the components to restore your security system to functionality; it sounds like they attempted to wire a permanent resistor into the ignition to "spoof" the BCM.
That is why the yellow wire was disconnected, they didn't "forget to hook it up" because it is part of a harness that is either plugged in or not plugged in; this is a common bypass for a dead VATS system but $2000 is enough to easily buy the new tumbler and keys; if they charged you 2k for a hack that they didn't even do correctly you need to stop using that shop.
Your options are.
1) pull the column apart and restore the wiring to stock, then replace the key tumbler and do a security relearn.
2) pull the column apart and do the resistor hack correctly, then do the security relearn.
3) find someone with a program like HPtuners that will go in and disable the VATS system permanently in the programming (this is the best solution for an old creaky VATS)
If done correctly the resistor hack is pretty reliable and costs about 1 dollar, but the number of people that cannot seem to get that hack right is astounding; your story is not uncommon.
That is why the yellow wire was disconnected, they didn't "forget to hook it up" because it is part of a harness that is either plugged in or not plugged in; this is a common bypass for a dead VATS system but $2000 is enough to easily buy the new tumbler and keys; if they charged you 2k for a hack that they didn't even do correctly you need to stop using that shop.
Your options are.
1) pull the column apart and restore the wiring to stock, then replace the key tumbler and do a security relearn.
2) pull the column apart and do the resistor hack correctly, then do the security relearn.
3) find someone with a program like HPtuners that will go in and disable the VATS system permanently in the programming (this is the best solution for an old creaky VATS)
If done correctly the resistor hack is pretty reliable and costs about 1 dollar, but the number of people that cannot seem to get that hack right is astounding; your story is not uncommon.