I would diagnose the throw out bearing by taking off the bell housing dust cover, detaching the clutch cable from the clutch fork, and then pulling the clutch fork back so that the throw out bearing no longer makes contact with the clutch pressure plate fingers, if this makes the noise stop it is almost certainly the throw out bearing.
When I put a new clutch and throw out bearing in my car there was a noise from the throw out bearing when the clutch was not depressed, it ended up being that the clutch cable had a bit too much slack and was allowing the throw out bearing to slip against the clutch pressure plate fingers.
So you might try adjusting your clutch. If your car still has the stock clutch quadrant this can be done by lifting up on the clutch pedal with your foot when the car is turned off.
When they installed the new engine they may have neglected to properly grease the throw out bearing and the retainer it rides on, they could have also incorrectly installed the throw out bearing on the clutch fork causing it to make noise. Of course it could just be the throw out bearing went bad, or something else like the transmission input shaft bearing.
I have inserted a picture of the dust cover and clutch fork that I mentioned, this is on the drivers side towards the front of the car.
Good luck, and welcome to the forums.