I replaced my starter back in November and ever since there has been this clicking whenever the car is started, but will only click when the engine is cold, once the engine warms up it only makes a slight clicking avery 2 seconds. Also if you have the car in gear and hold the brake and rev just a bit there is that same clicking sound. It is really puzzling me.

Any idea where it might be coming from? Upper end (lifters, most likely), lower end (harmonic balancer, unlikely)?

well it is coming from around the Alternator most of the time, and sometimes up around the PS....i really don't understand because when i shut it off it never made this sound, changed the starter and then started it and it started doing this and the sound is coming from nowhere near the starter.

Does the noise increase in speed with engine speed?

yeah when it is cold it does increase with engine speed

The most likely culprit is a lifter. But I have a very light tick in my '95 that is probably valvetrain other than lifter, that has pretty much driven me mad. Maybe it is a bad valve spring or rocker arm, though they all looked good when I inspected them when I changed all my lifters trying (unsuccessfully) to get rid of my tick. If you find out what yours is, let us know!

ok ill get to invesigating and report back when i have a clue

Thats the first guess - lifter not getting enough oil.
Exhaust manifolds can also click when cold.
This is something you have to keep looking and listening for.

To add onto that last post, take a close look at the manifolds for cracks.