Ok after about 12 hours of experimenting and googling I was finally able to get through this quest. My main is level 71 and this was very frustrating as all I wanted to do is finish this quest and continue adventuring and getting the last 5 achievements I am missing. My solution required cheating and console commands, but at least I was able to advance this quest. I take consolation in the fact that I can destroy Miraak in 1 dual wield attack anyway. This is PC only.
First fight to the point where you get glitched and Miraak is stuck ethereal.
In my game he was stuck 1 level below me in the center of the map.
"This step is only required if you want his loot"
Open the console and use the TCL command for no clipping.
Go down one level and you will see Miraak just standing there invulnerable.
Open the console and use the kill command. You type kill then the actor ID. Supposedly you should just be able to click on the actor and get the ID. In my experience this is inaccurate. Google Miraak and try the various ID's on the wiki's. The first two numbers vary depending on the content you have installed. Eventually you will find the correct ID and he will drop dead then you can loot him. I'm pretty sure the
UESPWiki was the more accurate of the wikis.
At this point you have to use setstage DLC2MQ06 550 This will advance the quest to the point where it says you completed. You will miss the cut scenes but at least you can advance the quest. I watched them on youtube so I don't feel so bad.
Now you're gonna still be stuck in Miraaks world (whatever it's called lol)
Use setstage again. I'm not sure what number advanced the quest but I tried 560, 570, 580, 590, 600, etc. Eventually I hit the correct number and the book spawned in the middle of the platform.
At this point you can read the book and reset perks and read it again to leave the zone as normal. When you exit immediately save the game so you don't have to go through this nonsense again and can continue playing normally. Hope this helps someone. This was really irritating me as I have over 500 hours into this game mostly on one character, and I could not advance without cheating.