I had the exact same problem. I just wanted to post what I did to fix it in case anyone else has the same issue. Problem: What happened was after kicking Miraak's butt he goes ethereal in the middle, his health goes back to full, and he stays there. As for the dragons only 2 dragons can be seen. The missing one is Kruziikrel. He's the problem. Solution: 1. Use dragonrend on Sahrotaar and kill him near Miraak for him to absorb the soul. 2. Push the tilde key ` to bring up the console 3. Use tcl to turn off colision 4. Use player.setav speedmult 500 to give yourself a speed boost 5. Run over to the dragon still flying in the sky, open the console again, click him and then type disable and hit enter. He should disappear. 6. Run way back over to the place you first met Sahrotaar. Kruziikrel should be lying dead there. 7. Run back to the book that takes you to the previous chapter of the dungeon and read it to go back. 8. Then click the book again to go back to the area you were just in. Kruziikrel should be warped to where Miraak is. 9. Run back to where Miraak is and open the console, click Kruziikrel and type resurrect and hit enter. 10. If Miraak doesn't kill Kruziikrel then kill him yourself. This should allow Miraak to absorb the last soul he needs and continue the fight. If it doesn't work try letting him absorb the dragon you disabled. I couldn't because he was bugged and wouldn't respond to anything I did to him so I disabled him.
