As far as #2 goes, I'm not sure why that's happening. It should work. CGI.pm should be good enough. Now, for #3 that's a known issue with CGI::Application::Plugin::Apache on mod_perl 2. I've had the fix in my code for a while but just haven't uploaded it to CPAN. I have repented and it's now in the PAUSE queue, so it should be available soon.
-- More people are killed every year by pigs than by sharks, which shows you how good we are at evaluating risk. -- Bruce Schneier