What next?
 

I want a decent handleing car. I still need the front shocks but so far I have: Kenny Brown super subs, H&R ss springs, Steeda Strut tower bracer, Bilstein rear shocks, steeda Quad shocks, and 17x9 rims with z rated tires. Is there much else I need for a nice handling daily driver? If so what is next other than the Front struts.

I'd get some caster/camber plates also. After that and the front struts you will have a solid foundation for handling. To go much further with it you need to make some choices and part with alot more money. If you want the ultimate in handling you need to get a tubular k-member up front with revised geometry such as Maximum Motorsports, Griggs Racing, or Kenny Brown. Also, for the rear you will need either a torque arm/panhard setup like Griggs or MM, or the Steeda 5-link to get rid of the horrible stock design that binds when you try to corner.
With the parts you named that you already have you will probably notice that you can overheat the stock brakes pretty quickly now on windy roads. Either a Cobra or Baer front brake kit will take care of that. I've actually seen the Cobra front upgrade for under $400 for rotors, calipers, and lines here: http://www.mustangracing.com/.

My brakes over heat really really fast. Is the Cobra front kit any good? I plan on getting that adventually but not sure if it was worth it.

The Cobra kit is excellent for the money. Unless you plan on driving alot on the track and hauling down repeatedly from high speeds, it is probably going to be sufficient. I went with the Baer Track Kit, which is based on the same setup except the calipers are lightened and I got the cross-drilled, slotted, and zinc washed rotors. It cost about $300 more than the Cobra kit, but looks sweet and sheds heat a little better. I attack the windy backroads around here towards the coast and I have never overheated the Baers even with 15-20 minute stretches of repeatedly hauling down from about 80-100mph for 20-25mph corners. (I still have stock back brakes, by the way). Another thing that really helps keep brakes cool is ducting some air to them. The 2000 Cobra R has an awesome carbon fiber setup that puts the air right through a hole in the splash shield, but it's really expensive, so I'm trying to cob together my own homemade ducts.

Where the side scoope is on the 94 and 95 there is actually vents. On the 96-98 it is not real. I am not sure if this is what you are talking about. I do not know how much it works.

The rear suspension is the limitation on a stock car...after you fix it up the front suspension will need to be addressed. I would start off with a set of lower control arms with spherical bushings in at least one end (and ideally a 3 piece in the other end if it has a rubber/urethane bushing), such as MM or Pro3i's. Next up I'd look into a panhard bar, to stabilize the rearend in the corners. If you want faster transitions from corner to go, a torque arm would be next, although this is not a critical step on a street car. After all of the rear I would start back up front with a K member, control arms, and coilovers, but there's no way I would waste money on any of that before doing the rear.

Hey blue00gt
 

Those brakes you posted are they factory? If so do you know what year cobra? It says '03 but the '03 cobra has brembo rotors I thought.

They are supposed to be what comes stock on a Cobra, but what year Cobra I don't know... Might wanna give them a call to find out for sure.

You could add some ploy bushings to the front control arms, and likewise to the steering rack.
Then further upgrades might include a whole new k-member and tubular control arms ($$$).

Brakes are a HUGE difference. They are also an investment! As I upgraded from 4-lug to M2300K Cobra 13" brakes, wheels,tires. OUCH!
See my site for photos...

blue00gt that you so much for Cobra brake link. I just ordered them.Thanks for all of your other help also.

My pleasure. Have fun with it - the brakes will give you alot more confidence when you are hauling butt coming into the corners.