I have an Apache 2.2 server running mod_proxy and I would like to manipulate the output before the proxy sends it down to the client, but I need something more powerful than mod_substitute. Is there a way I can run the proxied content through something like mod_perl so I can modify parts of the output?
Yes, you can use mod_perl Output Filters :
https://perl.apache.org/docs/2.0/user/handlers/filters.html#Output_Filters