I have a 93 cobra mustang that was flooded.and I have a 5-speed behind it and I think it Is locked-up.

There are 2 rods inside the transmission that had each gear on. The upper rod which is also the input shaft that goes through the clutch has 1, 3, 5. The lower rod that sits right under it has the other gears on it. Each one of those rods have bearings on each end. The upper rod may bearing may be bad and may have come apart inside the trans.

Well if it is flooding, either something is shorting out the injectors and causing them to be wide open, or one injector is stuck open, or you have a pressure regulator leaking liquid fuel into the intake.
Are all of the spark plugs wet ?
Can you start the engine if you disable the injectors ?

check for corossion on the asd relay.

a special tool goes in the line at the connection to release the lock you can get them from any auto parts store

can it be done? Yes. is it easy? No. While the basic design of the engine is the same, they are completely different. The cobra in 2003, had different heads, intake and rotating assembly. Also the 03 cobra is an ODBII vehicle while your 93 model is ODBI. i have seen several mark viii's that retained the stock engine, but bolted on the cobra intake. It requires some modifications but is relatively straight forward. hit up some of the mark viii forums, they pictures and in depth discussions on how the swaps are done.

start by removing the the shifter lever and boot, next remove the drive shaft,then remove clutch cable or hydraulic line for throw out fork,it may be neccessary to remove y-pipe and some of the exhaust using a transmission or floor jack support transmission and remove crossmember, remove bellhousing bolts and transmission should now be free to remove.

ok. so you know the fan is good. switch out the relay for that fan with another same relay and check with the a/c button.

It will be on the passenger side of the tranny about half way up.
The bottom plug is the drain plug and the top one is the fill plug.
You will fill it to the bottom of the fill plug,it will hold around 5.6 pints.

Open the trunk, the reset switch is behind the drivers side tail light, or inside the rear fender area, behind the interior trunk liner. There should be a small place to put your finger through the trunk liner to reset it, without taking anything apart.

your car has a ford AOD-E if it's an automatic, if it were a 5 speed manual it would be a T-45, the T-56 is a 6 speed manual transmission that was found in the 2003 and 2004 cobra models.