Even though the configuration GUI isn't working yet, I've went ahead and uploaded the Homunculus AI package.
http://www.shrinemaiden.org/fate/hatonlinere/HatOnlineRE-HomuAI-5-7-2013.zipUnzip this to your Ragnarok Online folder. To enable, type /hoai until it says "using customized AI" or something to that effect and then rest and resummon your homunculus. By default it is passive, to switch it to aggro mode hit Alt+T. Hit Alt+T again to go back to passive.
RAIL saves its configuration in a statefile. The statefile is located in your Ragnarok Online folder and is named RAIL_State.homu.lua. Here's documentation on all its options:
https://code.google.com/p/ro-rail/wiki/StateFileIndexIf you make changes to the state file just rest and resummon your homunculus for them to take effect.
Right now the default state file has priorities configured for Ant Hell 1 and Orc Dungeon 2. Excluding those listed maps, in aggressive mode it will automatically attack anything in the search radius, including things well beyond its ability to kill so be careful running around in aggressive mode.
Some settings you may want to change are the max search radius and assist behavior. The radius your homunculus will check for targets is currently set to 14 cells, and if it is beyond that it will automatically come back if you start walking. You can increase it by changing the rail_state["MaxDistance"] line. Do note increasing it dramatically increases system resources and can cause heavy client lag if set too high. It will not assist your target and will stick to listed targetting priorities. If you want it to assist you, change rail_state["AssistOptions"]["Owner"] from "indifferent" to "assist". The homunculus will automatically defend you above all else and will go passive on its own if its HP is below 10%.
Another handy option set you might want to change is rail_state["RunAhead"], rail_state["ActorOptions"]["Default"]["KiteDistance"] and
rail_state["ActorOptions"]["Default"]["KiteMode"]. If you have an Amistr or Lif, setting RunAhead to true, then setting a KiteDistance and KiteMode to "tank" will cause your homunculus to run ahead of you and draw aggro and maintain it by kiting at the specified distance. If the target then changes to attack you, it will then close into melee mode and start attacking until it is the main target again. It's also useful if you have a homunculus with a ranged skill like Vanilmirth. I have a Vani and I have KiteDistance set and KiteMode set to "always" so Vani will always kite and only use Caprice to attack. Setting KiteDistance to -1 means it'll never kite and will always stay in melee range of its target.
The AI already has sensible defaults for skill usage, but if you want to tweak them, run the AI at least once so the AI can detect which homunculus you have and populate the default settings. The AI will autocast all buffs as soon as it can, like for example Lif will use Emergency Avoid whenever it can. Amistr will castle if you're under attack, and Vanilmirth (and Lif too probably but I didn't check) will attempt to heal you if you are under 25% HP.
I have no clue if it's been updated for Homunculus S skills or not but I would assume not. I will probably have to do some work expanding the AI if that's the case.