Originally Posted by joshgsr_325 (Post 6467839)

Ok, so I'm pretty good with cars but this is my first mustang and I've never experienced any of these problems with the 20 something other cars and trucks that I've owned. So I figured I'd ask you guys for your expert opinions.
It's a completely stock 2004 GT 5spd with 57,000 miles.

1. The car wobbles or rocks up and down at low speeds. It's always there but it's really noticable in turns. That wobble/rocking turns into a really bad vibration throughout the whole car at highway speeds with the clutch in or out. Had a friend ride next to me and he said he didn't see any of the wheels shaking and everything else looked normal.

Check shocks, likely shot, they really are only good for abou 50k miles. Also, i'm not 100% sure I understand your description or the problem, but this defintely sounds like what happens when you install a new clutch without resurfacing/replacing the flywheel.

2. There is a lot of vibration in the shifter under acceleration. When not accelerating the shifter kinda jumps around a little...definitely more that it should. There are a lot of clanking noises coming from the tranny area when i shift or hit bumps. Also, theres a "clunk" when I coast for a second and then give it gas.

Is the shifter stock or an aftermarket Short Throw? Vibration is normal, think muscle car. The clunk is because you have a beefy ass drivetrain, and this happens in all of them, however, if the noise is VERY loud, check the U-joints, they could be worn prematurely. Also, check to see all bolts are secured in driveshaft couplings/U-joints.

3. last one...on cold starts the engine knocks really loud for a couple of seconds. It also idles a little rough all the time. oh yeah, and the rear end whines at 55mph.

Oil pump may be going, though its a long shot given the low mileage, be more descriptive of the "knock" sound...it could just be the lifters, this is common after setting for a very ling time or after an oil change. But it should go away in a few secs. And it shouldn't happen again the next time you start it.
That's it...I think. It is tune-up time so that could have something to do with the idle. As for the vibrations and noises I've been over the car a hundred times and the only thing I found wrong is that the right front wheel has a tiny little bit of play from left to right and that's accompied by the inner tie rod "clanking". I'm certain the throwout bearing is a goner because when I let the clutch out in neutral it gives me that metallic his sound. I've had it in a couple of shops and they can't seem to find anything wrong with the car. I've replaced the tires, had alignments, serviced the rear end and tranny and use synthetic oil and none of the wheels are bent. Its my daily so I take really good care of it but the car still rides and handles like ass and it's driving me crazy because I can't find the problems other than the ones I mentioned. I know those would have some effect on it but it shouldn't be this bad. Anyways, sorry for the long post, I just wanted to give you guys the full story. Thanks in advance for all your help.