as for cleaning, I like to have some small rags to stuff the ports in the head( intake ports ) to avoid getting anything into the combustion chamber... and I like to have the Lifter valley covered with a towel, again to help avoid any debris... From there I used a scraper first, followed by a cookie( 3M Abrasive pad ) on my air angle grinder.. Followed with Acetone or Brake cleaner to clean the metal of any oils..
The cover that you are referring to does cover a coolant passage... Its not common for that cover to spring a leak... And about the only time you'll ever get a gasket for it is in a head gasket kit.. You might be able to get that from a dealer, but I have yet to see that cover leak on an L27, Thats not to say it could never happen, just simply in all of the years I have messed with 3800's I have never seen one leak..
as for the lower gaskets, yes they can be overtightened and become crushed.. This is the reason you will not want to overtighten the bolts.. Take the time to clean the intake bolts and use some Medium Grade Thread Lock( Blue ) when installing the bolts so that they will not back out..
Being that you have made it this far you must be Mechanically inclined..
And your saving a good chunk of $$$ too..