2. Non-optical quality neutral density sheets from Roscoe or Lee can be used to cut a set of custom-fit, above the lens filters. I did this with my Zone VI cold light head specifically to increase my exposure times. (I like smaller prints.) Placed them inside the round housing, above the diffusion sheet. Or, optical quality density neutral filters can be used below the lens.
3. Yes, AN glass on top, fuzzy side down in contact with non-emulsion side of the negative. Some carriers include a clear bottom glass (my Omega D5 ones do), while some (LPL, I seem to remember?) use no lower glass. For 35mm negatives that usually have a slight concave bowing on the lower emulsion side the bottom glass is often not even required.