If using Servos then, if the drives are capable of analogue control (+/- 10v), I would recommend the IP-A rather than the IP-S.
The IP-A is slightly more tricky to get set up due to having to tune the axes in both drives and IP-A but the end result will outweigh that by far.
Regarding your questions
1.you would probably be best talking to mmoe as he has done a Shinx router which may be similar to the machine you are contemplating doing.
2. You assign the slave in the CSMIO plugin, I have never done it but it looks straightforward enough.
3. With the IP-A you can easily use the Index pulse from the encoder to give you very accurate homing, you will require a separate home switch for each axis and also limit switches (for safety, although not strictly required but recommended). What happens is you tell the machine to home, it moves until it sees the switch then backs off until the switch closes and then it seeks out the Index pulse of the encoder and stops and sets that as home position.
You can do similar with the IP-S but how exactly will depend on your servo drives. If your servo drives have an open collector output for the Index pulse then it will be straightforward and similar to the IP-A. If however your drives just have line driver output for the Index then you will need to make up a wee circuit.
CS-Lab suggested to a friend how to make that circuit and I made one for him, and also one for my own use on the wee lathe that has the IP-S, it works great
To contact mmoe you can get his details here
http://www.machsupport.com/forum/index.php?action=profile;u=36077and you can also see his build on the CNCzone, here
http://www.cnczone.com/forums/general-cnc-machine-related-electronics/182484-retrofitting-shinx-cnc-router-csmio-ip.htmlHood