You probably caused the CEL by popping open the injectors. I've caused a CEL or two myself over time by experimenting. Clear the codes & see if it resurfaces.
(edit: after replacing the fuel filters)

i havent touched the injectors at all. What does CEL mean?

You didn't do this? :confused:

CEL = check engine light

whoops, yea i did that...it was a while ago though and the check engine like didnt come on until about a month later.

Surprised noone has yet asked what RPM the engine is idling at.

this is something weird that its doing.

If you are at a light and hold the brake and bring the rpms up to 1k and leave the rpms there without touching anything, the car will change the rpm speed up and down 2-400 rpm at a time for some reason. Anybody know why it might do that? It may lead me to believe it could be a sensor of some kind?

alright guys I've been searching and reading for a while now and I've found a lot of threads of people having the same problem, but none of them had answers! It seems like they were all throwing parts at their cars and never fixed them.

Anybody know what I should do here? I don't want to take it to a shop and have them throw parts at without knowing if its going to fix it?

I'm going to grab my volt gauge and check the voltage at the battery, sometimes cars act funny if the alternator is weak and there arent enough volts in the system. I doubt thats the problem but i'm out of ideas on what to check.

This may be unrelated but it's a good thing to do anyway.

Have you ever replaced the tank screen?

Also...

Do you ever let the car run below a 1/4 tank before re-filling?

I'll explain when I hear your answers.

havent replaced the screen, and i do let it go below a 1/4 tank. When the tank is low there is no difference in how the car works.

also fuel economy is down
there is a strong diesel exhaust smell coming out of the exhaust when the car is idling

also i didnt change the prefilter. Where is that located?

The pre-filter is to the left of the main filter as you face the engine. Opposite side of the housing.

What "mis-fire" code did you get and what scanner are you using?

I asked about the tank screen because I recently ran out of fuel at just a little under a 1/4 tank. I also have an increased vibration at idle. My current theory is low fuel pressure at idle.

All of this has set in somewhat suddenly, over the course of a couple months. I'm working on replacing the screen now.