1. My guess based on what he says about Orpheus (which is where the story falls apart) is that he can only be independent inside the artifact
2. I think he wanted them to incubate so the thralls would be able to use illithid powers. Which is why he only comes to us at the last minute. He wasn't really saving us - we had finished cooking and it was time to turn off the oven. I think he was hoping to the let the pods cook us for a few more days
3. Dunno. He knows the Gith will find him?
4. He wants to kill the brain so it won't make him a thrall again. Which I'm 99% certain is the answer but which also makes his decision to join the elder brain make approximately 0 sense.
5. Good question, no good answer
6. Good question, no good answer