What year is your bike? I think the three pipe bikes had the cat in the cross over pipe. The two pipe bikes had the cat in the pipes, so if your bike was originally a two exhaust pipe bike then the TORs have eliminated the cats. If you have a three exhaust pipe bike then you will need a new crossover pipe to eliminate the cat.
If the dealer replaced the pipes they usually retune the bike with a Triumph approved "TOR" tune.
RamAir is a popular upgrade to the intake and will perform best if retuned to take advantage of the increased airflow.