5000 must be some sort of mistake. Balmung hasn't gone over the 4000s that has been reported. That being said 3500 is about 90+ mins.
Also ques are to be expected and suffered. That is normal. Disconnects are also normal. Having a shit npc instance when you can't afford to have enough instances not so much.
Some other people are saying they have 5k ques as well. How is this possible?