Ok here's a few more links but it sounds like most of what you need has already been supplied.
#1: Learn C# or some other medium/high end programing language (C++ is awesome but it's a hassle for alot of people to learn, Java is great but again... not as many resources around the forum for it)
I recommend C# simply because there are a ton of conquer online sources written in C# and they give you some great examples on how to code things (they are basically half of a proxy mixed in with a bunch of other features already... so it's good inspiration)
#2: Learn about packets
#3: Learn about Conquer, it's packets, how the client/server communicates.
Sources are another great example as well as asking around some.
#4: Cryptography!
The auth/login encryption is quite basic and has already been posted around here... Blowfish will be a bit more work (game server encryption) but again.. lots of information about it already posted and some completed codes (rippable form various sources, the wiki and the forum)
#5: Put it all together into something that works properly. Very useful if you understand first how a proxy really works and what you are trying to do... here's a basic explanation.
Proxy will bind itself to a specified port and listen for connections (coming from client). On client connection the proxy will send a connection request to the Auth/login server. It will then handle communication between the two (while modifying packets being sent if necessary) Client->proxy->Server and Server->Proxy->Client.
Once auth/login procedure is done you will switch over to the Game server (the ip and port for which can be discovered from one of the login packets coming from the server)
The game should be now trying to connect to the ip/port provided in that packet (you should have modified it to connect to the proxy on a different port). The proxy will then accept that connection and forward it to the game server. You then setup the game server encryption (using data being sent between the two + some packet modification from the way I understand it) and then forward data between the two while intercepting/changing any packets you desire along the way.
You can then handle actions such as botting through packets being sent.
Eg: Handle chat packets being received Client->proxy. Pull commands from them and respond with the appropriate action (such as jumping to a specified coords.. this requires sending a packet to the server and updating the client)
Hope that helps a bit.. You will need quite a bit of coding knowledge though before you can really do much with a custom proxy... Best of luck though
Pro4Never