Don't be so hard on yourself. Coming back from an injury is no easy task, no matter how much you train. Creaks and groans, little pains and soreness, all will have an effect on your lap times. 12th is not a bad start.
I've found that unless you are at the peak of the sport, your bike has very little difference on your lap times. With that in mind, I would consider ensuring your suspension is as good as you can get it. Use the Race Tech guide to get the right spring rates for your weight, ability and terrain. Use the gold valves if you can afford it. Other than maybe a flywheel, I'd leave the motor as stock as possible but tuned (jetted) perfectly (of course, buy quality parts with all repairs i.e. Boyesen Reeds, FMF Pipe etc.) as any change you do to make it more powerful will also make it less reliable.
I'm here to tell you that you can come back after injury, never win another race, yet still win the championship. I did - a couple of times. I didn't win another race for 11 years.