Id say you have done it right. invested your money over the past 2 years on the important things. Now that you have the equiptment along with some experience under your belt, you can now appreciate and feel what a better upgrade can do for you. So many people get a new bike and then want to go hog wild on upgrading this or that, when they dont even know why they are upgrading it, let alone be able to feel the difference.

I agree with wheels for now.
Saddle only if your saddle isn't working for you. No sense in changing it up if it isn't creating issues. If it is and you want to go specialized, it wont cost you $300. you can get the specialized Romin evo pro with carbon rails for under $200.