Finding the End city

I think that the best solution is just to remove old map of the END and let it generate again - by new methods of generation and also with new dragon and cities.

The thing is that even main island is generated in new behaviour, which may be the problem why even after another kill of dragon you won't find any portal or so. (It may be just bugged inside of blocks or so, or it may not even be there)

You can do it by deleting region files from your save, but be sure you are NOT in that dimension and that you will lose all buildings in the end. For being sure, make a backup.

Wiki:

The End is saved in the same way normal worlds are, in the DIM1 subdirectory of the world save.

Deleting the DIM1 directory will reset the End, and all man-made buildings will be deleted.

Pros:

• You will get the new main island with new towers
• new dragon
• no glitches due to different "old generation" and "new generation" of terrain
• after defeating the dragon you will get outer islands for sure, too.
• New blocks will be generated even on main island

Cons:

• You will lose any buildings in the End

Yes but you have to spawn a new ender dragon after you've updated to 1.9.

Players can re-spawn the ender dragon by placing four ender crystals atop the exit portal, one on each side.

ender crystal craft guide -> http://minecraft.gamepedia.com/End_Crystal

after respawning the dragon and killing it, a portal will spawn