First off, I am cross-posting this from Server Fault because I did not receive any responses there. If that is against the rules, I apologize.
What sort of issues could(should) I expect if I were to install 5.3.6(VC9 only) with a VC6 compiled version of Apache?
Sorry, no personal experience, but this ServerFault article gives some hints.
Problems that could occur are described in this answer.
This install description may also be of help.