I have both wakaba and kareha installed and running under suexec installed with next to zero problems. The one thing I can't workout is this.

==> /var/log/apache2/error_log <==
suexec failure: could not open log file
fopen: Permission denied
[Wed Jan 09 15:24:42 2008] [error] [client xxx.xxx.xxx.xxx] Premature end of script headers: paint.pl, referer: http://xxx.xxx.xxx.xxx/o/wakaba.html

==> /var/log/apache2/suexec_log <==
[2008-01-09 15:24:42]: uid: (1001/dood) gid: (100/100) cmd: paint.pl