There are a few things about mod_perl 2 that you should know. First and foremost: Apache::Request doesn't work with mod_perl 1.99 yet. You can directly use $r if you so wish. $r->hostname, $r->get_server_port, $r->uri, and $r->args can be very helpful if you wish to get the current URI. However, you'll need to add quite a bit of code to get the same functionality as either Apache::Request or CGI. You can use CGI as long as you use Apache::compat.
In all, I wouldn't suggest migrating to mod_perl 1.99 yet. The documentation is sparse and there are still a few bugs. Still checking out mod_perl 1.99_11 to see if some of my concerns are still there. I hope this helps you with your problem.