2000 Saturn SW2

I have a 2000 Saturn SW2 manual tranny. When I start the car after its been off for a while, it makes random (i.E. No rhythm) clicking/(light metal on metal?) Sounds, and sound like its coming from the front of the passenger seat side area. This occurs in low gears and once the car has been running for about 10 mins. Or so, the sound goes away. The clicking occurs when I shift gears the most, and also a little bit when i'm not shifting too. Thanks so much for any help you can offer! I really appreciate it!

my friend thought it was the exhaust manifold, but when I brought it in to the muffler shop, they said that was fine, but I did need to repair a crack in the intermediate exhaust, which I did. But that didn't change anything. I don't have a mechanic yet who I know is reliable, so I'd love to maybe have some idea about what is wrong before I get charged by a shop to start figure out what is wrong. If its not serious and isn't causing damage/problems, then I'm not so worried about it. Thanks!