1. Getting conjunctions working. Haven't seen any pop up just yet. If anyone has any ideas here, please let me know. Using Innerspace and ISBoxer.
You can assign key strokes to the colors, look under the key bindings in the options menu. I believe they are under the "Fellowship Maneuvers" section (I'm at work now so I can't check for the exact name) and they should be named "Top", "Bottom", "Left". and "Right" rather than being named after the colors.

I have a multi step action in IS for conjunctions that sends the key bind I set for the color I want, one character at a time. So when a conjunction pop I hit the key 6 times. That way you can set up the more complicated color combinations. If you just wanted all the same color you could set it up much easier.

Conjunctions will not pop on normal mobs, they need to be Signature or higher, and are random. Guardians and Burglars get abilities that will start a conjunction.

2. Is there a way to have the music just play on the main screen instead of on every instance of the game?
Use IS to virtualize the settings for each of your characters, and then you can turn the sound off on each of their clients and leave it on your main character.

3. For looting items during quests do you just have everyone select the target and everyone try to loot it? Eventually they all get the correct amount of items this way? Or are you having one loot at a time? Seems like it would be easier just to have the loot key on one button, have everyone assist you and then try to have them all loot. If one person needs something he gets it.
One thing I noticed with mobs that drop quest items is that if you loot the mob on your main character and after looting they still have the mob targeted that means there is loot on the mob for other characters. If after looting you lose the target on the mob there is nothing on it for another character. That can be useful for quests where the drops are not 100% for everyone in the group.

I send "F" to the slaves to assist the tank, and then "U" to loot the corpse. I let them all try to loot rather than switching screens to do it individualy.

4. Can the Minstrel heal everything? Diseases, poisons and whatever else happens? I know there are other healers, but want to try the Minsrel first as long as that class can heal everything.
The Minstrel is a good healer, they have the direct heal and a group heal. I'm pretty sure they cannot cure everything though. They get a fear cure, and other classes take care of the other detremental effects. Hunters get a poison cure, and LMs get disease, and wound cures.