will that cause my check engine light to throw codes?

 

no...unless you previously had an o2 which went into the cat and you didnt put it back on...

 

when i swapped the CAT i swapped the stock o2 sensor with just a bosch brand name o2 sensor, but according to the diagnostic check, it doesn't like something to do with my exhuast system

 

so you put on a new high flow cat with an aftermarket o2 sensor correct? And now your throwing a cel regarding your exhaust system. I think you answered your own question. Try puting the oem o2 sensor on and see if it goes away. Try putting the stock cat on with the bosch o2 sensor. If you get a cel, its the o2 sensor, if you dont, its your cat (which i doubt).