I know I'm digging back a few months in resurrecting this post but I must have missed it when you first posted up.
There are quite a few choices for pipes available for the Thruxton, I've used D&D's, and currently am using the Triumph "Off Road Only" silencers. The D&D's are
LOUD, the Triumph pipes are more mellow, almost neighbor friendly. The D&D's do make better power, but not enough to offset the noise they make. Neither pipe requires carb re-jetting by themselves. As a matter of fact I am running a K&N in the standard air box with a modified snorkel, the inside of the snorkel cut off so that only the mounting flange sticks in the air box. The spark plugs run a nice chocolate brown, right where you want them. It was too lean, and there was too much intake noise with the snorkel fully removed.
Today, I had a revelation with my latest mod. I got a really good deal on an aftermarket ignitor box (ECM) and installed it today. My bike, like most Bonnies and Thruxtons, has been very cold natured ever since I have owned it. With the new ignitor box it starts so much better, didn't even need to use the "choke". I don't know if it modified the igniton curve, they really don't give you much information beyond the rev limiter being set 1000rpms higher, but it does start, hot or cold, much easier. I'll post up if there are any issues down the road, but so far I'm liking it!
Here's the website:
http://www.rmstator.com/en/index.php/Motorcycles/Triumph/all_triples_2000-2003/High_Performance_CDI/1433
Ignore the fact that it says "all triples 2000-2003", it's for the Bonnies and such.