aluminum ds for 99 cobra
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The FMS "J" shaft will probably fit your car. It won't fit an 01, since the transmission is longer, but there will likely be 1/4" of clearance between the rear extension housing and the slipyoke.
Get it and try it. The worst that can happen is that you'll have to take it to a COMPETENT shop and have it shortened 1" and rebalanced, which will cost about 70 bucks. The cost of the shaft and rebalancing combined is still far below what Griggs and PST charge for their shafts.
Why do you want an aluminum driveshaft for your car? You might want to see my webpage below before you make a decision.
Get it and try it. The worst that can happen is that you'll have to take it to a COMPETENT shop and have it shortened 1" and rebalanced, which will cost about 70 bucks. The cost of the shaft and rebalancing combined is still far below what Griggs and PST charge for their shafts.
Why do you want an aluminum driveshaft for your car? You might want to see my webpage below before you make a decision.
I hates to tell you 
but the Ford Racing Aluminum Driveshaft does fit in a 99 Cobra. I say this becuase I have it in mine, and it took the shop only a few minutes to do it (once my x-pipe was out of the way). It's not that expensive either, so just go ahead and order the FR one, I don't know who told you it won't fit, Ford just never got around to updating their part's description I guess. By the way you will never even know it's even there, not sure if thats a good thing or bad
but the Ford Racing Aluminum Driveshaft does fit in a 99 Cobra. I say this becuase I have it in mine, and it took the shop only a few minutes to do it (once my x-pipe was out of the way). It's not that expensive either, so just go ahead and order the FR one, I don't know who told you it won't fit, Ford just never got around to updating their part's description I guess. By the way you will never even know it's even there, not sure if thats a good thing or bad I have a question for you Lo pony...When I got my 99 Cobra last year, it would vibrate at around 75mph, the feeling I had was just what I had been reading about many other 99 Cobra's. But after reading your link on driveline vibs, Im not so sure if that is what I was experiencing. But I went ahead and ordered a FR aluminum driveshaft and had it professionally installed by a mustang shop. The vibs at 75mph went away, so I just assumed they installed it correctly and the driveshaft did its job. My question is...Would I likely cuase more vibs and noise if I change my gears, even though my aluminum driveshaft works perfectly fine now? Im assuming nothing will change when I put the gears in. Because I have heard that if gears are put in correctly, they will not make any noise at all. 
If you have no vibrations at any speed now with the aluminum shaft, you "shouldn't" have any after new gears if you take extra care to line it back up with the output shaft and the pinion flange just like you have it now.
About the fit issue, some cars DO actually have a problem with the fit because of production tolerances. The reason Ford doesn't list a driveshaft compatible with the 99-01 is due to the fact that these IRS cars are extremely sensitive to imbalances in the drivetrain - there's a real problem with vibrations. If you are unlucky and the aluminum shaft is a bad match for your flange runout tolerances, it will vibrate. Ford doesn't want to take a chance of that happening, so therefore they don't want you to replace the driveshafts with aftermarket ones.
About the fit issue, some cars DO actually have a problem with the fit because of production tolerances. The reason Ford doesn't list a driveshaft compatible with the 99-01 is due to the fact that these IRS cars are extremely sensitive to imbalances in the drivetrain - there's a real problem with vibrations. If you are unlucky and the aluminum shaft is a bad match for your flange runout tolerances, it will vibrate. Ford doesn't want to take a chance of that happening, so therefore they don't want you to replace the driveshafts with aftermarket ones.
It "looks" like the FRPP shaft. FRPP uses the weld on end caps like the picture of that one there. Steeda doesn't specify whether or not it will fit IRS cars. It's certainly more expensive - the FRPP J shaft is 155 bucks from gene evans ford (www.gefracing.com). Call Steeda and see if they make a driveshaft "SPECIFICALLY" for the 99-01 Cobra with IRS. If they say it's the same shaft for all the 96 up 5 speed cars, then order the 4602-J shaft from Gene Evans for 100 bucks less than the Steeda one.
