Didn't see in your OP but did you verify all your glow plugs are working? That is where I would start if you're having rough start issues. If the timing was off I would think it wouldn't run well once you got it started but that is just IMO. Check our your glow plugs just to make sure their in good order. I had 2 out on my car and it would start but took longer glow cycle to get it going. Replaced all five and we're back in business. Make sure you ream the holes the glow plugs thread in to if you end up replacing them.

If you've been running bio for awhile the spin on filter might be ok. If you have been running primarily dino diesel and just switched to bio I would advise to change out your spin-on for good measure. They're cheap and don't take too long to replace. I would only do that if Bio is new to your car or it's had a good "stint" on dino diesel and now back to biodiesel.

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'98 E300 Turbo "Juliette"
'85 Federal 300TD