not sure, what your problem is: is it slow or does it "crash" where the term "crash" is sometimes used for an uncaught error message in the browser and sometimes for a disappearing server process.
i got the impression from posting #8 that it is slow. even if the number in "db_exec: longdb 214670501 ..." is a time in microseconds, this is quite long. This seems to be some custom query in "sieca_modules" (whatever this is) which is not part of dotlrn.
The message from the referenced chat "timeout waiting for connection" is nothing to be worried about; it simply says that a connection thread stopped because it did not receive anything to do in the specified timeout interval. The sentence about the "db pool" is maybe from a wrongly configured db, but has most likely nothing to do with your problem, since you could connect to your database (... "I can add new courses...").
my guess is that something is substantially wrong with the "sieca_modules", maybe some indices missing, etc.