Well by the looks of it, the only part of your skill set that seems to be lagging behind the rest of your skillset is you database knowledge. Perhaps getting well and truly familiar with Oracle might be a good idea. It's very widely used and as far as I know is commonly used for larger projects. Then again you might consider (I think it was called) cloudscape. It's a database that is both embedable and capable of being used on a stand alone basis. I know you're probably thinking "What's the point of that when MySQL is the same anyway?", but cloudscape is a database written in java, so I'm guessing that might help in integrating a database more seamlessly with your java applications.
There's not really much else I could suggest because I'm still rather unskilled at the moment and haven't had the chance to get my hands on some real large scale projects, but I hope I've at least given you some ideas.