When you take the clutch bell off you would have seen a couple of shims along with the bearings.
If you look at this link you can see the clutch bell, bearings and shims just so you know what I mean.
http://cgi.ebay.co.uk/Hobao-13-Tooth-Clutchbell-Bearings-Shims-Hyper-7-8-/150443616690#ht_500wt_1182
If you don't have enough shims the clutch bell will have too much movement back and forth.
I know if I plan on taking my engine out before I run the car next and just screw it in any old way, I get this metal noise due to the gears not being meshed properly.
If your unsure on how to mesh the gears correctly, check out this video.
Hope this helps.