Runs Rough In The Morning
 

I recently replaced the #5 and #6 glowplugs after doing 1 thru 4 before winter. I took the IM off and the #4, 5 and 6 hard lines for easier access. Now, when I start it in the morning the motor, misses, shakes and idles poorly after it sits overnight. It drives away fine, no misses. I finally got all the air out and it stopped nailing. When I start it anytime during the day or when I leave work, it starts and idles perfectly.
What's up?

Two likely possibilities:

1. Something glow plug related.

2. Fuel system getting a little air in it when it sits overnight.

I'd check #1 first.

Ad one more.
If the Valve/s in the Fuel Supply Lift Pump are not sealing the Fuel will drain back to the Fuel tank and the Lift Pump sort of loses prime.

Does the problem go away or improve if the Fuel Tank is full or if the rear of the Car is higher than the front of the Car when it sits overnight?

The below Fuel Supply/Lift Pump is similar to yours.

New Style fuel Supply lift pump rebuild
http://www.peachparts.com/shopforum/diesel-discussion/288883-om606-fuel-pump-rebuild.html

I will turn the car around and move it down the driveway where there is more slope and see what happens. Tank is 3/4 full right now. The car sat all weekend with a full tank and did not run any smoother on Monday morning.
I will look into this though.
Thanks.

Did you remove the small return lines on the injectors when you removed the hard lines?
Those small lines can leak air into the fuel lines and cause rough starts and NOT look like they are leaking externally. If they are more than a few years old, order a meter of fuel line and replace all of them.

really? I've not heard this.
I was under the impression that the only issue these lines could have is lost fuel.
Hmmmm...

They are hooked into the main return line which in turn are hooked to the injection pump.

Ditto...

Return lines between injectors were replaced in the fall when I installed reconditioned injectors (Monarch nozzles) from Sean Watts :D
Yesterday morning it idled much better upon start up. I recenly filled the tank. I'm wondering if the previous tank was slightly contaminated?

check your fuel Pre-heater. Mine sucked air and problems started out like this and got worse. they are known fail points.