I dont really think they shorten the tranny life, during a normal shift the clutches slip and engage slowly, which is why its smooth, but they wear much faster that way. So it actually eliminates some wear.
As for the cat, I picked up a cheap one off Ebay for around 45 bucks. If I could do it over again Id get the Magnaflow/CarSound units that are about 60, theyre a higher quality piece.
Im not positive what size you need for a 3.8, youlll need to measure. The downpipe on the 3.5 is weird, as the pipe that you see is actually just a shield for a smaller pipe within it, I orded a 3 inch in/out unit, and my exhaust guy made it work, but I think it was actually a little too big.
Dont get an oval shaped one as it wont fit in the opening for the cat, youll need a round bodied one with proper measurements.
heres one that would probably work
http://cgi.ebay.com/ebaymotors/Magna...2em118Q2el1247
You would need to measure and make sure the 5 1/8in width will fit in the tunnel shaped area. I think it will though, but id measure first.
Also, all Intrigues from 98-02 came with the 4T65-E transmission.