Tom,
I had a similar experience with my 41, and it appears the major problem is with the flexible gold connector connecting the CPU board to the main (keyboard) circuit board. Make sure there is enough pressure on this connector, or all kinds of screwy stuff can happen.
The other flexible interconnect (the one to the batteries & external ports) can also be problematic. Bad connections here can cause one or more ports to stop working.
While you have it open, check all the screw posts for cracking, and also check the back cover to ensure there are no cracks where the screws go - this can also lead to insufficient pressure on the contacts.
Despite all I said about sufficient pressure, don't overtighten the screws, as that can lead to cracked posts.
Use 91% isopropyl alcohol or a contact cleaner pen to clean the contacts while you are in there.
One last pointer - if you get some crazy results after you put everything back together, try shorting the battery contacts or leaving the batteries out for several hours, as stray charges can cause problems.
Good Luck.
Ed