You aren't alone in having those feelings: I travel by myself a lot and have felt exactly the same at times. As I suspect WillTravel was suggesting, the isolation can come in large part from not chatting with people -- as much as one enjoys independence and solitude, it can be really important to interact with others. For me, the situation tends to be worst when I'm in a country like Japan where few people can converse with me. After a while, I really have a need to hear a person with whom I can can have any sort of conversation (listening to CNN or BBC World just doesn't do the trick).
Also, I find Tokyo to be just about the most daunting big city on earth. It is hard to find your way around, and it is easy to be come disoriented. The only saving grace is that Japanese people seem to be universally willing to try to help a lost gaijin. Also, if you do get lost, there is zero chance that you'll inadvertently walk into a dangerous neighborhood.
If there's anyone back home that you chat with regularly, give that person a phone call. Sure, it'll cost you a few bucks, but it would be fun for both you and him/her just to say hello. If the hotel you're staying at has a nice lounge or bar, you might want to have a drink there and chat up someone who's there, especially someone who wouldn't take it as some sort of come-on. It wouldn't be surprising at all if another Western solo traveler would appreciate a chance to gab for a while.