1. Practice your tyre tube repairing before you go. Use only the tools in the kit you plan to take.
2. After a couple of trips where I weighed myself down with a toolkit like the kitchen sink I went for this
http://www.advdesigns.net/f800gstoolkit.html It's expensive and people exclaim over the price but just try pricing your time and the tools to fit a complete set under the seat and its value starts to become apparent.
3. I bought 2 Motion Pro alloy tyre irons with the combo ring spanner ends (One 24mm for the rear wheel, one 12/13mm combo for other stuff). With the 24mm spanner, you can leave the big 24mm socket in the kit, at home. I can get these levers under the seat as well as the adventure designs kit! However I also like a big steel lever and have to find room for this elsewhere. Three levers makes tyre changing rather easy.
4. Take a spare chain quick link or two. Break in the new DID chain that was suggested before you go and adjust any slack as necessary.
5. Ensure you pack your spare inners where they can't be chafed against something that will wear holes in them
6. Notwithstanding my lightweight tool kit, I like to find room for a pair of molegrips.
As you say you are doing only 3000 miles, chances are you won't need any of this stuff but you might be able to help someone else out!