I did some checking around the internet for information on the side gear fit in the case for Dana 44 axles. The Dana Spicer information lists no specs it just states "the case bore for the side gear should be round". Perceptible elongation should be minimal at best. Other folks that have rebuilt them and done the measurements on the side gear and the case ID bore all agree that the clearance is about .005". My best guess is .005" to .006" for clearance. Someone will have to measure them to see what the clearance and out of round might be. If they are not out of round or tapered, the surfaces are not scored or burned blue, and clearance is reasonable, then they are good to go. This is a semi floating rear axle so the stuff has to be free to move in there.
If you haven't already, remove the brake drums and inspect in there. Check the axles for smooth movement and play. If brake parts are secure, everything moves OK, axles are smooth to turn, and doesn't have much play, I'd run it. Clicking in a rear axle usually means a broken gear tooth or a bad bearing. Whining under torque load indicates a loss of preload on something and it's moving around too much under torque. If your not seeing any of this, you may have a problem somewhere else.
The only reason I would buy a junk yard axle is for the hard parts like the axles or housings. The gears might be good and they might be worn out.