First off, welcome to the forum Frank. You've come to the right place for the answer to everything that is Crossfire.
The Cedar/Slate interior is absolutely the best choice for the interior imo.
Our 04 just turned up 45k last night, and the only warranty problem we ever experienced was the rear hatch vacuum leak. (There is a detailed explaination on how to fix it yourself if neccessary, here on the forum). Oh, and the dealer replaced our 4 year old battery under warranty as well.
As mentioned, the 6spd. can be "notchy" between 1st. & 2nd. gears, and is very common, and as long as it doesn't "pop" out of gear, or is hard to get into reverse, you should be OK. Many owners mention it feels as though it gets better with more miles.
The clutch question is impossible to answer since every driver determines how long it will last. But unless you "side-step" it on a regular basis, it seems to hold up well.
The door rust problem is universal, (even if you live in the dessert) as long as the car has ever been washed, or in the rain. It really is a very simple repair to do at home (as long as it hasn't gone on for a long time). But it could work in your favor if you pull out the rubber seal at the bottom of the door and show it to the sales manager at the dealer where you're trying to buy the car. Pretty hard not to discount the price of a car (with rust) in Texas.
I'd make the "sticky" ignition key repair the deal breaker. I understand it can be an expensive fix at the dealer. But there is also a detailed explaination (here on the forum) on how to repair it also.
Your Son is a very lucky young man to have a Dad like you. Even though the Crossfire offers enough performance to get anybody in trouble very quickly, it is one of the best handling, fastest stopping 2 seat cars out there. Being a 2 seater is a + when it comes to teenagers (less distractions) and the car seems to withstand crushing accidents quite well.
Here on the forum there has only been two incidents resulting in fatalities in a Crossfire being reported. One in Russia "being T-Boned" at an intersection, and the other was when a fellow decided to drive his roadster off the edge of the Grand Canyon.
Good Luck