We have a 2006 Mack MR 688 that's running rough we have replaced injectors and the fuel supply pump. The truck seemed to run better for a bit but has now gone back to running rough again. I also checked my muffler to see if it had fallen apart inside causing restriction as well as the air intake cover is not causing restriction. Any help or ideas would be very helpful ! Thanks 

Any fault codes? Seems it would have to be fuel related because its a diesel and has no spark.

Any knock or smoke clues?

No real clues. I agree it seems to be. A fuel issue. I'm wondering if their is a sensor that tells the  injectors proper timing . The truck doesn't seem to pour the smoke out it seems to run very clean little to no smoke from the exhaust. 

Maybe too clean, is the electronic malfunction light on in the dash?

The electronic malfunction light only comes on when I have the PTO engaged doesn't flash just stays on steady. The light doesnt come on while driving. 

lift pump bottom right side of engine.  replace right away it will let you down completely .  Is the engine starting a little rough.  Turns over longer than normal.  Let me know. give me a shout cous

You probably know this but, if the malfunction light comes on shut off the cruse button and hold down on the cruse set botton the EML will blink and give you a code on what is malfunctioning. I'm sure your fuel filter has been changed (once mine had water in it and would freeze after stopping to pump). Maybe check for a crack in the fuel supply line?

Lift pump is referred to as a fuel supply pump we replaced it. We got the codes when the EML flashed they were for injector issue cylinder 1 2 and 6 so The injectors have been replaced. What about the inside of the fuel supply line collapsing inside ? Anyone ever here of this ?

2006 engine may have a bad EGR valvle .

its the wiring harness the plug going into the ecm 

when you say you replaced the injectors, did you just replace the mechanical injectors in the head or also the eup's along the passenger side of the block (the individual electronically controlled injector pumps for each cylinder)?   In my experience, faulty injectors in the head rarely Make the malfunction light illuminate.   A faulty eup will though    i'd suggest changing the three eup's you mentioned (you can do it yourself and have the dealer program the trim codes if you don't have a vocom or equivalent tool).   They are more than a grand a piece unless you find reman or aftermarket.    

Merry Christmas everyone!    

I replaced the eup's as they are the electrical component of the injector system from the Mack dealer. The truck runs strong when it wants to the shudder that it gets into comes and goes when I'm off and on the throttle driving. Most of the time while pumping it runs smooth rarely getting into its stubble/shudder.

How is your turbo? Are you making boost. Any boost leaks I know with my ma  2006 sounds like it's studdering when first leaving a light and the turbo is not spooled up yet. But both my trucks do it so I'm guessing its like an anti smoke. So it holds the fuel back until the boost comes up. Sounds like a fuel or boost issue to me if it pumps fine but acts up while driving tap a boost Guage in the manifold. Hope that helps 

Check your alternator, all sorts of neat shit happens if your batteries or alternator are weak.  Also you mentioned malfunction light comes on when in pump gear, have you checked your ground speed sensor. If it is going it will dumb down the engine and put it in limp mode then all of a sudden it  goes back to normal.  However that should flash a code at you

Have you figured it out yet?  It can be, although incredibly rare, the o-ring underneath the jake brake solenoid - and to make it more confusing, mack doesn't sell it as an o-ring for the jake, it's an o-ring for the rocker.  Take out the Jake solenoids, and dig down with a pick to the bottom of the hole.  There's an o-ring down there which seals the bottom (pilot) of the Jake brake.  This happened to me on two different mack trucks (an '06 and an '07) last year.  It's hard to diagnose through these short messages, but if it occurs completely randomly but most often when you're trying to give it a load (pedal to the metal), check these o-rings.  Also, if it's hard starting, replace the pressure valve for the eups - it's not a pressure relief, it's a low pressure valve making sure you have at least a certain psi at the EUPS all the time.  If you don't know where it is, follow the fuel drip line (spaghetti noodle line) backwards.  That drip line clips onto the valve which is also where the lift pump pressure line goes into the motor.  You need that minimum pressure, especially on startup.

No we haven't resolved the issue 100% yet. The eup's that we put in were a big help truck pulls a lot better but every so often it gets into a fit and seems to stutter or run rough for a bit then decides to come out of its stutter and give full power again! The idea with the Jake/engine brake solenoid is intriguing I am unsure as to where I would find the solenoid. Any direction as to where I can find it to replace or at the very least inspect the O ring would be a big help! We have no issue with initial start up the truck starts and runs well as it gets warmer performance seems to drop off but again is not consistent as to when or how long it will stutter/run rough for. as for engine malfunction lights no more have occurred since replacing the EUP's.

They are in the rocker assemblies.  Take off the valve covers and there is only one electrical component in there.  That is the jake brake solenoid.  Follow the electrical wire (only one in there) and it leads you to the solenoid.  Take it out.  Down at the bottom of the hole that the solenoid's in is an o-ring which seals between the rocker and the jake.  You have to dig down with a pick to get it, but it's there.  

Based on the info here, and how confusing the problem seems to be, I would definitely say replace these o-rings (one jake brake under each valve cover, so there's 2) and see what happens.  Last one I did was actually in 2 pieces, so maybe you'll see something wrong right away and be certain.

sometimes if your injectors are bad or weak it will run, but run rough as well. We had a few newer units that had to go back to mack because they split the injectors.

Well I finally had time to dig into the exhaust brake solenoids and change out the o-rings with no luck truck still running rough but seems to be less frequent with the solenoid o-rings changed out. Yes I changed upper and lower rings on both solenoids. This is getting frustrating !

That's too bad.  Have you checked your coolant system with a simple pressure test?  If not that, then I'd swing by Mack and see if software needs reloaded/upgraded.  Good luck.

I think that may be the next step. Is to actually head to Mack and have them plug into it to see what is going on. 

Well we finally got our 2006 Mack down to the doctor ( Mack dealer) she was given a valve adjustment the injectors were rebuilt ( not the e.u.p's ) and the e.u.p trim codes were adjusted as well as a EECM and EEVM software update was installed. Drove the truck back to our shop and it performed very well fingers crossed that is the answer. Thanks to everyone for your tips and advice on this matter we definitely considered everyone's input in this matter thank you !