If I understand your question correctly, you want to move from apache to apache2 and from mod_perl to mod_perl2. Specifically, you are intreseted in compatibility. I've been running mod_perl 1.99.09 (long time, yes) with no problems, and I have several hundred CGIs running under Apache::Registry.

I believe the best advice is to use lexical variables; the rest will be taken care of for you.

Note: I've been keeping up with mod_perl mailing list. Be extra careful which RC tarball you get, there are major API changes between RC4 and RC5.