1. Adding turbos on diesel engines will have positve effect on torque output and a little help on horsepower rating. Some manufaturers claim 20% additional output while others have claimed to achieve 40% more torque.
2. Cylinder head manipulations from the basic port and polish finish, multi-angle valve seats to the more expensive stress relieving should atleast add 5-10% more. While some of you may read this in a wrong way; yes these techniques are also applicable on diesel engines too. ;) If I may add, a full engine dynamic balancing can reduce excessive vibrations on high rpm's. Everything can be achieved, the only downside I could forsee is the engine's durability.
3. Though skimming the flywheel on its contact area about 8-10mm will only help transfer the power quickly to your drivetrains, I didn't find any percentage of additional power output from this end. As I could remember 3-4 years ago, it was impossible to lighten the flywheel. Less torque, eventually no power to drive the whole vehicle.
But some local machine shops now claim that it is possible now for diesel engines. Though I would not recommend it as there are no studies or anyone to his flywheel claimed that it is 100% effective.
4. Adding a less restricted airflow filter means that the engine can breathe more than its usual. But be warned that a free flow muffler is not always as effective as the ads declare. Even on gas fed engines, the back pressure the original muffs make is a necessity for an engine to build up on its torque. Some engines may adjust the low end torque to 200-500rpm while other engines lose all the low end that it needs to move a vehicle from a standstill point.
5. There are two vehicle components that can achieve regearing. Transmission and differentials. All gears can be re-geared to suit the driver's need, more acceleration or more top end speed. Though you only have to choose either of the options mentioned. There's no vehicle yet that could have better acceleration and at the same time gain more top speed. That's why people occassionally adjust the turbo for acceleration then re-gear their system for full speed.