Using bootstrap (or similar) could be an option if you have a lot of messages or alerts. You can simply implement the pieces you need to get the alerts and such working with your current code, you don't need to implement all of it. Or you can create your own. Either way, there will be what sounds like enough work to go through creating some javascript or server code along with styling to get what you desire.
One more thing to note, in v7 you're limited with what you can do without customizing the out of the box webparts and controls when it comes to things like this. In v8, it's all transformation driven and makes your design and changes much easier to handle. I'm not saying upgrading is the all time fix, but it sure could make things a bit easier.