There's been a lot of people asking around about the valve adjustments on a DS1000, and how it is different from a regular 2v Ducati. Here are some notes to help supplement the valve adjustment information out there.
Please note, this is not a full tutorial, you can find tutorials on how to adjust your valves all across the internet.
The location of the timing marks are not the same, however the idea remains. When all the tick marks on the belt side line up and the tick mark on the flywheel lines up, the forward cylinder is at top dead center Compression (TDC-C).
Excuse the blurry picture, but the vertical cylinder's mark is at the 12 o'clock position. There is a tick mark on the case that corresponds to the cam's timing mark.
Once the belts are lined up, you have to make sure the front cylinder is at TDC-C. You can line up the belts, but still have the flywheel off so you would not be at TDC-C. This scenario just means you have give the cams another full turn to line the flywheel up. There is a physical arrow, and a black hash mark on the flywheel.
On some DS1000 motors and defintely DS1100 motors there isn't a visible sight glass to line up the flywheel and find TDC-C. Instead there is a bolt that you have to remove, sort of an inspection cover. You can also physically inspect the piston to be at TDC once the belts are lined up.
You are now ready to remove the belts and begin the valve adjustment.
Once you completed the forward cylinder, you can move onto the rear cylinder. The first step is to turn the cam so that both your intake and exhaust valves are disengaged. I've seen some motors have a hash mark indicating this position, but my particular bike doesn't. If you do have one, it should be on the inside case in the same general area as the photo shown below.
Once your cam is set, you can use the rear wheel and bring the rear cylinder's piston to TDC. This will keep the valve from dropping into the engine by accident. I do this by simply putting the bike in 6th gear and wiggling it with my toe and just peering into the spark plug hole until i see the piston reach TDC.
Yes I know i have a very dirty bike!
Now you can perform the valve adjustment on the top cylinder.
If you are reading ahead before doing your adjustment then great, if not then you will be wondering why you cant slide over both rocker arms to check for binding. Well don't go ripping out your hair just yet! the DS1000 doesn't allow you to slide over both rocker arms. You can only slide one side at a time. To check for binding you just stay with one side and check for binding in the 90degree range that you are allowed to move your cam. If the closing shim is too tight, you will immediately notice that you CANNOT slide the rocker arm back over. If it is just slightly too tight, the rocker arm will slide over, but there will be excessive drag on the cam as you spin it.
Another note is that the motor isn't the easiest to work on when its in the bike. But there is a little trick to help make this a quick 1 man job! To help keep the rocker arm down as you are removing the closing shims, you simply jam a 8mm allen key into the opposing side to jam the cam in place. You will need something at least 8mm thick. Anything smaller wont do so well.
The procedure for doing this is to depress the closing rocker arm for the side you are working on, and insert an allen key on the OPPOSING side. The allen key will fit right under the spring on the left side.
Once you do that the closing rocker arm will stay down and the valve is free to move. Some people use a forceps, which i don't understand why. The valve is not going to go anywhere with the piston at TDC. If it does drop, it will hit the piston. Now if the piston ISN'T there to stop the valve, then it WILL drop into the head.
Another thing I recommend is to swap to MBP collets. They are easier to install since you know their orientation unlike OEM half rings. They are also built to extend your valve adjustments since they are less likely to deform.
That's about all the notes that I have regarding DS1000 valve adjustments. Aside from these details everything else is pretty much the same as other DS1000 motors.