I have replaced leaking fuel lines, primer pump and have bled all the air I can out of the system as far as I can tell.

I still have a very rough running engine.

I haven't replaced the tank strainer yet but I will within the next few days.

Could it be my injectors?

All of this happened right after I ran out of fuel.

My shutoff problem was caused by a loose vacuum line. The pump and shutoff are fine.

What about running out of fuel would spur the rough running if not air in the system?

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1993 W124 300D
-297K on the clock as I type this.

Sounds like our cars are siblings. I battled a very rough a idle what seems like forever. I replaced the filters and rubber fuel lines (and switched supply and return lines to check) and still the pre-filter is only half fuel. Today, I bumped up the idle and all is well. I can't believe how many turns I had to make on the idle screw to raise the idle. I used a 14mm crows foot wrench to loosen and tighten the lock nut. Again, I can't believe how smooth it idles now. I don't know what the idle speed is though. I don't know how this can be checked.

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Brad
1981 300TD - daily driver
1963 Chevy II
2001 F-250 7.3 Power Stroke

Based on the smoke I am putting out I am fairly certain that my problem is that I have bad injectors.

Once I get that issue sorted out I will check the idle.

If you still have that much air in the pre-filter then you are getting air somewhere. Once I sorted out the old, cracked lines I had and replaced the primer pump all the air disappeared from my pre-filter.

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1993 W124 300D
-297K on the clock as I type this.

I've got a plastic jug with two hoses that I used once with a diesel purge. I'm going to hook it up and see what happens to the fuel level in the pre-filter.

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Brad
1981 300TD - daily driver
1963 Chevy II
2001 F-250 7.3 Power Stroke