I've had the same problems as you are having. I managed to fix the Server 500 error easily but not the best of solutions. With this problem your current php handler is not present or non-functional. Go into WHM under
Service Configuration->Configure PHP and SuExec
and change the php handler.
Here's my settings at the moment.
Default PHP Version (.php files) 5
PHP 5 Handler dso
PHP 4 Handler none
Apache suEXEC off
As for the other problem with File Manager under CPanel the directory listing is not shown - not sure how to fix this. (There are few search results from google for this term.)
ps: I am running WHM 11.28.52 [TRIAL]
CENTOS 5.5 x86_64