Did it run the same before the Valve Adjustment?
Is the Idle Seed set with in the limits on the Emission Sticker?
Is there any Smoke and if so what color is it?
How does it run when you are at higher speeds?
Try loosening the Oil Fill Cap at idle. If the rough idle goes away your Crankcase Breather system could be clogged.
Check the EGR Valve to see if it is function properly. Apply Vacuum to it at idle and see if it causes the Engine to stumble and lose rpm.
Get some longer 5/16" ID Fuel Hose and run it to a separate container of Diesel Fuel and see if it runs better like that. If it does you have a Fuel Supply issue to the rear or an Air leak.
Loosen and tighten one Fuel Injection Line at the Injector at time. This cuts the Fuel off to that Injector. Cutting the Fuel off to a good Injector causes the Engine to run even worse.
If you cut the Fuel off to a problem Injector the Engine there will not be much reaction to it not working. But, that only identifys a problem cylinder. To find out if it is the Injector you swap the position of the Suspect Injector with a good one. If the problem follows the Suspect Injector you know it is the Injector.
If the Problem stays with the Cylinder that now has the good Injector you have a problem in that cylinder of the Engine.
For More info:
DIY Repair Links
http://www.peachparts.com/shopforum/diy-links-parts-category/
http://www.peachparts.com/Wikka/DoItYourSelf