Please help!!!! Car has no balls!!!

I know absolutely nothing about cars. So I will try
my best to describe this.

2003 Ford Mustang convertable manual 5 speed
standard model

Once the car has been running for a while the
symptoms appear. They do not appear when the
car has just been started and only running for a
few minutes.
Symptoms include:
When in 1st 2nd and 3rd gear (if I can get to 3rd
that is). I can have the petal to the metal and the
car will have trouble getting over 40 KM/Hr. No
umph if you will.

If leaving the car in neutral (parked) but running, it
will eventually stall, almost like it loses power.

The temperature gage is also maxed out. It is over
heating. This JUST became known to me 10 mins
ago.

The car when being started makes a clunking or
clinking sound.

The car when displaying symptoms seems like it
has trouble um..., bresthing for a lack of better
words. It sounds like a freakin harley davidson
some times....

Turn the car off, let it sit for a hour or so and all
symptoms r gone until its running again for 20+
mins..

Thats the best i can describe it

Whats wrong with my car :(