Ok so I'm just curious if this is normal... I've had my car for a while but this is starting to bug me a bit. I'll just include way more information to see if I'm doing anything wrong.

So in the morning I'll start my car. The engine usually catches very quickly (like 2-3 seconds) and the rpms go to 1.75K-2.25K rpm in the idle which gradually dies down to 1.25-1.5K then briefly kicks back up another .25K rpm then drops back down. But anyways I'll pull out BEFORE the engine is warm (the temp gauge is still on "C" or sometimes even below)... I just wait for the engine to settle to 1.25K rpm and then I go (I shift at 3K rpm until the engine warms). Anyways I'll reverse out of my garage, then when I push the clutch in again, the RPMS jump to 2K.

So then I put it in first then go. I notice that when I push the clutch in while in first gear (ie to put the car into neutral or to shift to second), it feels really rough and makes a lot of noise. Like a loud clunking noise. It also happens in second gear too. I don't notice it at all in the higher gears and it mostly goes away when the car has been running for a while. Is this normal?

No - could be the loose pressure bolt fiasco. I would have the dealer inspect this ASAP.

if you're driving the car cold, then yes...it is normal. when you push on the clutch and the RPMs jump to about 2k, it's just the motor with no load trying to warm up. you'll know if the clutch is going bad when you start to grind gears more often, you hear "chattering/chirping" sounds when you get on and off the clutch, RPMs will rapidly rise when you hit the accelerator and the car doesn't accelerate. 1st and 2nd gear will always be a little harsher in the cold. since its a bigger gear driving a smaller one, it'll be more jerky and stiff until it warms up. you have nothing to worry about.

So then I put it in first then go. I notice that when I push the clutch in while in first gear (ie to put the car into neutral or to shift to second), it feels really rough and makes a lot of noise. Like a loud clunking noise. It also happens in second gear too. I don't notice it at all in the higher gears and it mostly goes away when the car has been running for a while. Is this normal? I notice that one as well, I just let the car warm up a little longer and it doesn't do it.

cool. thanks for the info guys. i might ask anyways when i take it in for my next oil change (about 700 more miles I think) to make sure it's not the pressure bolt or earlier if it gets worse. I'm guessing it is just the cold weather (though cold here is like 55 degrees), but it sounds pretty ugly and feels ugly. It's only like that for like 5 minutes though which leads me to believe it's just cranky after not being driven for the night.