Edited to remove an erroneous statement.
I use a dial indicator through the spark plug hole to find piston TDC. You can use wood skewer to find it also with some practice. On the 04 and 05 models, you can use a Locating Screw, part number 580.30.080.000, which screws into the front of the crank case. There is a small slot machined onto the crankshaft that the end of the Locating Screw fits into to hold the engine at top dead center. You can also remove the flywheel cover and follow the procedure Johnf3 describes in a previous post.
You have to remove the spark plug anyway to turn the engine over and have the piston stay where you want it.
There are 2 ways I use to turn the engine over to find top dead center. One is to remove the flywheel cover and turn the engine over with a socket or a spanner as Johnf3 did, the other is to put the bike on a stand in 6th gear, and use the rear wheel to turn the engine over.
The early models have marks on the fly wheel and the stator that you can use by looking through the inspection port on the flywheel cover. The 04 and 05 do not have any specific marks, but you can align the flywheel pulsing magnet to the pulsing coil per Johnf3's previous post to get near top dead center. Some guys make a mark on the engine case and on the flywheel once they have ACCURATELY found top dead center. This provides a handy reference for future Use.
So there, you now know how to find TDC! Just make sure you are on the compression stroke. You can tell that by observing the exhaust valves move about 1mm about 30 degrees before TDC as the automatic compression release actuates.
Make sure you use a torque wrench on the valve screw lock nuts.
Follow the instructions on page E5 and E7 of the Repair Manual, the Locating Screw is in the tool section of your Parts Manual
Hope this helps,
This post was edited to remove an erroneous statement about the absence of timing marks on the 04-05 bergs.
Joe