I thought mine already came with Java Script on it? Not positive on that though. For the bbmessenger, you're sure you have the correct PIN and all that stuff? I remember being a little confused about it at first, it wasn't even worth the trouble of me setting it up.
As for a messenger program, you should be able to download it from their site through your blackberry and then input your license information to unlock it for however long you bought it for. If you can, you might want to try and get a refund, and look into Jivetalk. It is a really sweet messenger program that can use MSN/AIM/Google and a bunch of other stuff.