IMHO, it's time to just check everything that you can just to be safe and sure the bike's tuned to the best it can be so to speak. It seems that you have a good idea of what needs to be done etc already. What about your DOO? What's been done to that, if anything? If you haven't changed her out I will bet the spring has zero tension on it and isn't adjusting the ballancer mechanizm correctly any more.
I'm not a fan of lubing cables myself, I feel that the lube attracts dirt to the cable and as a result clogs up the cable in the long run...to each their own on that....lol. I have 85,000kms on my cables and they are still working well without lubing them.
If the bike is running great then I would just maybe check the plug for correct gap and cleanliness and check valves once again, brake pads and the caliper movement as in even brake pad wear. If the carb is running fine and your mileages are still good then no need to clean her yet. Have a check of every nut and bolt for loose ones....augh!! Check the brake fluid levels. I would change your fork oils as I bet it is ready for a change if not already done. Take each fork off and empty and flush with varsol or paint thinners then again with auto-tranny fluid to get the thinners out all the time pumping the forks to get the cleaner and auto tranny fluid into all valving etc. Then fill them to the correct level once again. Check over the wiring for possible rub sections..? Check battery for fluids or if gel cell no need... check for cleanliness of battery and starter connections. If you haven't bypassed the safety switches if you feel it's important, do it now....they tend to fail after a while....
The steering head bearings need to be repacked with grease, top and bottom and then torqued to the right torque which is all you can push with the back of your pinky finger when the bike is off the ground, not very scientific but it's a great way to get the correct torque without using the massive torque wrench. Search it out either here or over at the World site, it'll be written by the Patman and it will explain it completely.
Maybe time to go into the carb and do the simple mods to it and the desnorkle of the airbox? KLX needle kit or the 22 cent mod with drilling the slider and set the pilot jet screw to 2 1/4 turns from gently seated.
I'm sure there may be more, but my fingers are starting to bleed...lol.
Hope this helps....