Easy thing out of the way, guy at Jiffy Lube most likely did not check your spare tire to see if it was low, most people never check that anyways. If the tire light is blinking for at least a minute after start up that is a different issue entirely.
When you brought the car to Jiffy Lube the second time to have them check the lights did they provide you with a print out or a record of what DTC (Diagnostic Trouble Codes) they pulled from the system? Because if the MIL (Malfunction Indicator Lamp/ CEL) was illuminated along with the VSC & TRAC (Which do come on when ever the MIL is tripped) there were codes stored in your system.
I would also want to see any freeze frame data regarding the codes if availible (which if they were catalytic converter related would be most likely available.)
The Toyota Dealership should also have provided you with a similar print-out record when you brought it to them a second time. These codes and data can be very helpful in diagnosing what the issue is. It could be that they used too much fuel injector cleaner and essentially confused the system and partially burned the catalytic converter. It is also possible that the cat can simply be brought back by driving it a good long while, and again it could be that the catalytic converter is completely burnt out and requires replacement. I personally would never rely on a single set of codes to deterine whether or not to replace a catalytic converter on any modern vehicle because of what can go wrong in how the system percieves the catalytic converter's health.
I hope the best and that its nothing too bad, but I would personally start looking at all the other data and get more information before I would make a jump to replace anything as cost intensive as a catalytic converter. Even as a dealership technician I will admit that the larger majority dealers replace parts and assemblies not do diagnosis and component repair.
Here's a post I made in regards to how catalytic converter monitors work and why diagnosing them can be tricky;
Catalitic converter lifespan