See here for some ideas:

http://www.peachparts.com/shopforum/diesel-discussion/354874-rough-starting-question.html

Like you I was hoping for the magic fixes that were supposed to come with such advice as adjusting the valves, rebuilding the injectors, and installing new glow plugs, and they all did nothing at all.

Also, if you split a piece of rubber hose and stuff it between the air cleaner and valve cover that'll cut that rattling (I have the same issue).

-Rog