Since it is most apparent after up load the gear (gear is already selected) it is possible you are looking at a transaxle bearing issue. Trying different brands of tranaaxle fluid will help, I know when I ran Royal Purple - it tended to make a bit more noise than my brand of choice, Redline. Some have come up with homebrew concoctions and mixtures of different gear oils that seem to really cut down on gear whine. Fine metal particulates in the oil is normal - but frequent drains and refills of the transaxle will help keep those from become a major issue (let the oil's additives do their job). Low oil would make the noise more noticeable - sometimes you have to drive the car a bit after replacing the oil before anything significant happens.
Sometimes the noise is not even related to the transaxle - another common source that causes a gear-like whine under partical load in the higher gears is the belt tensioner. There will be some gear whine, as this is a mechanical coupling - but the oil and transaxle case are designed to help reduce the amount of noise transmitted to the operator. I'd drive it for a couple of weeks or so - do another short drain and refill - and see how the noise level is after the miles start to roll on.
Just for curiosity sake - what else did they do when you had the clutch replaced? Turned down the flywheel? What brand of clutch/pressure plate was used? Did they adjust any linkages? Did they replace the bolts for the pressure plate and flywheel?