I wouldn't add water at this point. If you take a gravity reading pre-boil and at the end of the boil you could add water or malt extract then, depending on which direction you were off. I also don't worry about trub too much. The yeast don't care. It will settle out, and you can dump it with the hops and yeast at the end of everything.
There are worse things than ending up with less beer than what you planned for. I'd rather have 3 gallons of good beer than 5 gallons of bad.
On another side topic, it sure seems like you boiled off a lot of volume. I usually boil off a gallon per hour. This will vary based on the kettle one uses, but a gallon an hour is typical.