After a couple hundred miles the problem has reappeared. I'm fairly confident either the pump wasn't bad in the first place and I've just been very lucky for a couple weeks, or air is being let in from somewhere else. I can see bubbles in the clear line that runs from the bottom of the secondary fuel filter to the injection pump, and they would seem the originate from the IP itself. After a couple miles of driving I can see very slight seepage from out of the round things that connect to the hard injector lines. Might this be the cause?

Yes, this is probably the cause.

There should not be any fuel seepage...ever.
If fuel can get out, air can get in.

Can you post a photo of the "round things"?
I'm not exactly sure what it is you are describing.
Perhaps, you mean the fuel injectors??

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78 W116 300SD 'Desert Rose' new as of 01/26/2014
79 W116 300SD 'Stormcloud' RIP 04/11/2022

These things.

Ah, those are the delivery valve holders.

The air incursion leak is probably at the union where the ball of injector hard line fitting attaches to the cup of the delivery valve holder.

To test:
1) on a cold engine - clean the area both ends of the hard line injectors throughly with brake cleaner and let them air dry completely.
2) test for dryness by touching the tip of a dry tissue to the union of the injector hard line flare fitting with the delivery valve holder.
3) if the fitting is completely dry - run the engine for a few minutes
4) shut engine off and re-test for seepage at the union with a dry tissue.

If you find a leaky flare nut fitting, just tighten it a bit more with your flare wrench (17mm?).
If the fitting still leaks after re-testing, then disconnect the line clamps securing one hard line to the other, then loosen the injector hard line flare nuts with your flare wrench and remove the suspect injector hard line completely.
Inspect the end of the injector hard line that seats on the delivery valve holder for any corrosion, scratches or deformations that would prevent a good seal from being established.

Clean, repair(polish) or replace any damaged injector hard lines.
Make sure to cover the open injectors and delivery valve holders to prevent foreign matter from being introduced.

On reassembly, carefully start the flare fittings by hand to avoid crossing the threads.
Once both ends of the injector hard line are loosely attached, press the hard line onto the delivery valve holder and hand tighten the flare fitting.
Do the same with the other end of the injector hard line at the injector on the engine.

After the flare nuts are as hand tight as you can get, then tighten the flare nut with your flare wrench to avoid rounding the flare nut.
Re-attach the line clamps.
Re-test to verify the leak(s) are gone.

Hope this helps.

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78 W116 300SD 'Desert Rose' new as of 01/26/2014
79 W116 300SD 'Stormcloud' RIP 04/11/2022

It could also be air getting in at the secondary fuel filter, or elsewhere. There are 2 types of filter housings with different seals used in each. The best place to look for air in fuel is a temporary clear pvc line in place of the cigar hose (return to tank). It should have a solid, bubble free non foamy stream of fuel at all times, engine running or not (as in overnight and longer). Any air that gets into the system will end up there.

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85 300D turbo pristine w 157k when purchased 161K now
83 300 D turbo 297K runs great. SOLD!
83 240D 4 spd manual- parted out then junked

Have you pressurized the fuel system yet?

It is vital that you put it under pressure and find the fuel leak.

My bet is the secondary fuel filter can is rusted through.

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I checked the flare nut ends and found one that looked rather rough. I also cross-threaded it when screwing it down so it's getting replaced regardless. As to pressurizing the fuel system could you go into little more detail about what that entails? I know the leak is past the fuel pump so is it as simple as taking an air compressor and connecting it to the lines or is it more involved than that?

Alright after replacing that hard line no difference was noted. I then attempted to pressurize the fuel system. I clamped the return hose shut and then hand primed it. The only real leak was from the delivery valve holders. I suspect the last person to adjust the timing forgot to replace the washers. Would this be enough to cause this issue? I should also note that the bubbles I see in the line run from the pump to the fuel filter housing as though the leak originates in the IP.