Transmisson "Rattle"
 

So today while driving across a bridge (for sound purposes) in 5th gear going 35 mph (3.73 gears and 35's so around 1500 rpms) I noticed a noise that sounds almost the same as when the engine is about to stall/bog coming from the transmission. After paying closer attention the noise is present under light to mid load. Any ideas what this could be? If it means anything, I've been trying to pull out in 2nd gear sometimes and would get a similar noise so decided to stop and stick with 1st.

5th seems like an awfully high gear to be in at 35mph with 3.73's and 35's if you're trying to put a lot of acceleration load on the transmission.

If it's making the same noise when you're trying to take off in second, I'm guessing it sounds almost like a grunting noise, sort of a rattle. Drive in lower gears and downshift when you need more power.

If that's not it, get a friend to take a video while you drive, and post it up.

I usually try to keep the rpms under 2k when not accelerating. I'm just learning now I should keep the rpms a little higher if needing to accelerate. I think "clunking" would be another good adjective to describe it. It sounds like a more mild version of the noise when you don't give enough gas from a stop..just worried I messed the tranny up somehow as this is my first stick.

You are definitely bogging the motor down being in 5th gear at 35 mph. This puts the engine out of its powerband. You are not going to hurt the tranny running it under higher rpms.

That's not the tranny making that noise. It's your clutch that's going to burn out because of the driving habits.
The tranny can be taken out of the jeep and be thrown off a cliff to roll down a mountain side and all you'll hear is the sound of screaming critters and hikers.
Cool it's your first manual. Find a friend or co-worker to drive you around in it so you can get used to the FEEL of how manual should be driven.

Right around 2k isn't too bad for just maintaining speed. I'd keep it closer to 2k than I would 1500. Definitely run it out a bit more when accelerating. Putting too much load on an engine at low RPM is real tough on the bottom end of the engine (crankshaft, connecting rods, etc).

You probably haven't ruined anything, but taking off in 2nd gear especially with 35's and relatively high gear ratios is going to really accelerate wear on your clutch.

My first manual I owned* not the first I've driven it. I know how to drive it properly and was just wondering about noise not driving habits. Guess I'll just keep the rpms higher. Thanks guys!

THE noise is caused by your driving habits is what they are saying.

yupp got that. Higher rpms it is

Didn't mean to sound rude guys! I just thought as long as the rpms weren't below around 1000 I was good. Guess you learn something new everyday! Thanks a lot for the input.