A lot of good info here, but I want to make sure of some things. Constant noise, no change with rpm? More of a clicking or ticking as opposed to a knock you said also? Metal is never good in your engine oil, but small amounts are not uncommon. Most of the things in your valve train and even you engine block should change noise with the engine rpm's. A bad bearing, rod or main, a bad piston pin, valves, rockers, springs, all these things should make noise that was associated with rpm's.

You said the noise was low? I also heard you say 4 speed, stick? if the throwout bearing was bad or installed backward when the motor was put back in it would make a noise that didn't change with the rpm. It would also sound more like a clicking or ticking and would get worse over time. You would also probably not notice it in the way the car shifted, especially if it's still new to you. In case it's a newer automatic, a bad torque converter will make clicking, clacking noises as well as a bad u-joint. I have had a number of u-joints fail that stated like that. I think I might be looking at clutch stuff though. just a thought.