Dear A.,
You said your son has been sick but did not say if he is sick now or during this crying stint. The reason I am asking is that when my daughter was sick, the emergency room nurse gave me a tip that really helped. She said to put a phone book under the head of the mattress because if they have the sniffles they will drain at night and with their heads raised it helps the draining and makes them more comfortable. It also helps the ears.
The next thing with ear infections is garlic oil in the ears. it really helps.
Try feeding your son cereal or bananas before bed.
Also get him on baby vitamins. They go through growth spurts and the body is under incredible stress. B vitamins are proven to help with night terrors. But, never give vitamins at night, only first thing in the morning. This will help build the immune system. The healthfood store has really good liquid vitamins for young children. I have been giving my youngest vitamins from a very early age and now she is five and is never sick. Early on she was sick a lot, especially once she started day care.
For his room, set up a good night light, make sure closet door is shut. Maybe walking him around the room before bed and reading stories would help. Also try leaving his bedroom door open. It takes experimenting to figure it out. Most kids go through this and letting them cry did not work for me either.
Good luck.
D.