Well I am a professional software developer. I do this for a living. I wouldn't be worth much if I couldn't take something as well written as the bitcoin client and figure out how to modify it.

The main protocol port is in protocol.h in a function called GetDefaultPort. You should also change init.cpp so the help message matches the port you choose in the GetDefaultPort. That's for the protocol port.

The default RPC port is found twice in bitcoinrpc.cpp in calls to GetArg("-rpcport", ####) where #### is the default port of whatever coin you're using as the original source. Like the protocol port, it's mentioned in the help strings in init.cpp so should be changed there too.