So it seems things are falling apart with my daily driver . It is really very unfortunate that all these problems are compounding all at once. Now, not only am I experiencing strange cooling system and vacuum problems, but somehow, air is finding its way into my fuel system, and my in-line pre-filter is almost entirely air. I bled the lines via the fuel filter housing, which got most of the air out of the pre-filter, but then after just a minute or so with the engine running, the pre-filter is again almost all air, and the engine begins chugging, then dies, unless I rev it up a ways. Any guesses as to where the air is coming from? I'm not seeing any fuel leaks anywhere. The air has been getting in the lines for some time now, but never so much that it was starving the engine of fuel, before now. I figure maybe replacing all the fuel hoses should be my first step. I'm assuming the return lines end up back in the tank? If thats the case I'd think that any air in those lines would bleed through the tanks vent hose, and not end up back in the lines heading towards the engine. So then could I assume that the air is being pulled in from some connection between the in-line pre-filter and the tank. Maybe a clogged tank screen could cause the pump to draw air from a loose connection?

As you were thinking; change the Fuel Inlet Hoses and for a good measure change the Plastic Primary Filter also.
The 5/16" ID Fuel Hose that is sold in the regular Auto Parts stores will fit and is rated for diesel. In my area it only cost about $3-$4 for enough Fuel Hose to replace both pieces.

If the above does not help there could be some issue with the Hose back under the Fuel Tank or even the hard Fuel Inlet Tubing.
The section of Hose that is between the Fuel Inlet Tubing and the Fuel Tank Screen is also 5/16" ID. To change it the Fuel Tank would need to be drained.

You can use the regular 5/16" Fuel Hose but you need to grind of the crimped collar on the Fuel Tank Screen end to use it.

We forget that there is about 14.5 psi of Air Pressure around us all the time. This means that Fuel may not leak out of tiny cracks in the Fuel Inlet system partly because the Atmospheric Pressure helps to hold it in and parly becaues of the viscosity of the Fuel.
But, when the Fuel Supply Pump starts sucking Air can be drawn through the cracks.

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84 300D, 82 Volvo 244Gl Diesel

Yes, I'd swap out the rubber sections of fuel lines first. If you search on my name and 'emptying the fuel tank' you'll find instructions on how to dry out the tank before replacing the lines.
You could also be sucking air in through an old primer pump but I don't think that would fill the primary filter with air. There will always be an air bubble in the primary filter.
There was also a recent thread here from a member with a 116 SD who solved his air leak problems by replacing the lift pump.

You could test for the leak by putting a bottle of diesel fuel in the engine compartment and hooking it up to the primary filter and running the car. If the car runs fine that way, then you know the problem is upstream from the primary filter towards the tank.

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1977 300d 70k--sold 08
1985 300TD 185k+
1984 307d 126k--sold 8/03
1985 409d 65k--sold 06
1984 300SD 315k--daughter's car
1979 300SD 122k--sold 2/11
1999 Fuso FG Expedition Camper
1993 GMC Sierra 6.5 TD 4x4
1982 Bluebird Wanderlodge CAT 3208--Sold 2/13

You can Tee in a 0-30 pressure gauge between the spin-on filter and IP body line to see what kind of PSI you are getting to the IP....should be between 8-15 or so ...exact pressure numbers are in service manual....needle will bounce some at low rpm but at least you can see avg fuel pressure to fuel galley in IP....

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1978 Yellow 300D (The Mustard Toad)
1980 Blue 240D (The Iron Toad)
1989 Grey Mitsu.4WD Mighty Max Pickup (Needs a Diesel transplant bad)

(Open the pod bay doors HAL)

just had similar problem primary pump was shot, replaced and every thing fine.

Hey thanks everyone for the helpful ideas. So I replaced the fuel inlet hoses to and from the inline pre-filter and bled the air our via the outgoing hollow bolt from the fuel filter housing to the injector, and now it seems to be running fine! After warming up, and idling for about 15 minutes, occasionally revving it up, the bubble in the pre-filter grew in size a bit, but nothing compared to before, when it would fill entirely with air in just a couple minutes. So I'm thinking that air was making its way in through the old inlet hoses. I can actually see areas on the larger inlet hose going to the pre-filter where it was covered with hairline cracks. I figure since there is still an small increase in air in the pre-filter, one of the other hoses between the tank and the engine compartment might be the culprit. I'd like to replace them with viton for bio-diesel as long as I'm at it. Or at lease the one from the tank screen since its a specific hose. Will 5/16 ID hose do for the rest of the connections?

yes

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1977 300d 70k--sold 08
1985 300TD 185k+
1984 307d 126k--sold 8/03
1985 409d 65k--sold 06
1984 300SD 315k--daughter's car
1979 300SD 122k--sold 2/11
1999 Fuso FG Expedition Camper
1993 GMC Sierra 6.5 TD 4x4
1982 Bluebird Wanderlodge CAT 3208--Sold 2/13