I appreciate your military service, thanks.
The best mod for 99 and 01 Cobras are gears. If you do a lot of highway driving I would go with 3.73 or 4.10s. If you are love to smoke in more than 2 gears go with 4.30 or more. The next best mod on my 99, for performance was a cat back. I used the
magnaflow. I still run the stock H and cats so it is not too loud. I am sure an off road H would bring up the sound. Listen to flowmasters before you buy, they sound GOOOOD.
For a big improvment in driving, change the shifter. I have the tri-ax and love it.
I have heard good things about the MGW. It shifts good and is not as noisy as the tri-ax.
For CAI I ran the densecharger. It made a noticeable difference. It was a little cobbled together. I like the way the JLT, or what ever it is, looks. The smoother the flow the better results. I would stay away from metal tubes, my opinion.
If you have to pull the transmission, buy an aluminum flywheel. I bought the 2000 cobra r one. I think the 2003, 2004 Cobras will bolt in.
I bought the FRPP alum driveshaft. It says it will not fit, but it did. You can do the driveshaft if you are not going to pull your transmission any time soon.
When you do the gears be sure to add Fords friction modifier additive. It keeps the rearend from chattering in turns. Chattering will not hurt anything and might eventually go away, but you wont' like hearing it after you been in there working on it.
I put on JBA shorty headers, but believe them when they say it is not worth the work or money. The catback was more noticeable, seat of the pants pull.
I saved the best and most expensive for last. I put a 9 lb intercooled KB supercharger on.
With all the above mods, 4.10 gears or steeper you will really enjoy the car, but the KB is an experience you never regret.
It is EXPENSIVE. KB may have a military discount. Just to give you an idea, think over $6000.
It does come with everything you need. It is a complete kit. Do not consider less than 9lbs which is max for our stock motors. And do not cut corners going without the intercooler. It will take you a week to put the kit on. It barely fits under the stock hood and some kits rub a little.
I have listed the mods in the order that will give you most for the install.
If you know you will be going to the KB, no ifs and or buts, use the 373 gears and do not buy the CAI.
Just to give you the final results, I am making 430 rear wheel hp. This is instant power, not something you have to red line to see. It will break the tires loose in second just rolling into the throttle.
You can break parts if you go to big drag slicks. That is over 500 hp at the flywheel.
One other bolt I did was the pinion brace and bushings. Shop for price on it. Ford used it on the 03 and 04s also. Buy the poly bushings for it. The solid alum bushings are too harsh.
There are superchargers and owners that boast about more hp on the dyno, but on the street the KB feels like a 428 CJ from 2000 rpm to red line. You don't have to turn it up to 5000 rpm to enjoy the power.
buy ford gears, set up is a lot easier.
Good luck,
Keep in touch,
joe