Stuck With 2002 Mazda Protege Hesitation and Now Idle Shaking

I have a 2002 Mazda Protege 2.0L that's been reliable for almost a decade. I've only really had minor problems before this.

However, a couple weeks ago on Wednesday, there was a small amount of hesitation. About 5 minutes later, there was a rather scary bit of hesitation. I made it home. I did some research, and thought it's probably something with the fuel system. Since the Mazda Protege doesn't have a separate fuel filter, I speculated it could be the fuel pump that was starting to go.

The next morning, there was hesitation right away on driving. Going around the block in small laps, the hesitation was still present. It mostly would hesitate and then recover and keep going. Around lap 4, going uphill, I got a really bad hesitation and the engine stopped/stalled and for a period there. As I tried to keep going, the check engine light was on flashing. I had to reverse back down the hill, into an alley, and the check engine light was solid. I kicked the fuel tank, and it seemed to resolve the issue since I made it home. So I thought that settled it.

However, when the fuel pump arrived and after installing it, it didn't fix the problem. The fuel tank also looked really clean inside. I believe the new fuel pump worked and I had hope for a couple of blocks, but really I could feel the slightness of the hesitation even before that and knew it wasn't fixed. Unfortunately, in installing the fuel pump, the battery had to be removed, so the check engine light went off, and has never come back on again since.

A long long time ago (I think 2015) I had a funny thing with the air intake valve where it was bumped when a mechanic changed the oil, which exposed that it was leaking (a common problem with the Protege) caused persistent stalling, and had to be sealed up with duct tape. I thought perhaps it was the air intake valve leaking again, so sealed that up really solidly, and the problem was still present. I found one tiny line in one of the vacuum seals near the top of the engine and sealed that as well. I also cleaned out the air filter quite thoroughly. None of those fixed the problem, I don't see any other leaks anywhere on any of the vacuum lines, and in the process of attempting to validate those hypotheses with short test drive laps, during one of those laps, the hesitation got to the point where it happens just idling in the driveway.

The most recent hypothesis I had was the EGR valve. A couple of people suggested it could cause similar problems, and one reported that unplugging it has completely fixed their problem. It was a real pain to get to, however unplugging that doesn't seem to have fixed the problem. I also took a look at all of the spark plugs and adjusted their gaps, and couldn't find any issues there. The check engine light remains off and using the OBD system doesn't show any codes at all present. All the system checks seem to complete according to the scan tool. There's still plenty of oil in the system and it has been regularly changed previously. Other fluid levels are all okay. The fuel is half full, so it wasn't recently refilled (so I think that rules out bad gas but not sure).

At the moment, when I start the engine, it's violently vibrating. If I apply a lot of fuel leaving it in neutral, it seems like it isn't vibrating as much. I don't dare try to drive it.

I'm wondering what systems I should check next and how to troubleshoot this further because it really has me stumped.
 
The fuel pump housing contains the high pressure fuel filter.
The filter sock is the low pressure filter.


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Here's a link to the service manual for your car,..

 
I will post an update that the problem turned out to be the ignition coils.

After driving around the block some more times, the check engine light finally failed again with P0300 which is random/multiple misfires. That lead me right to YouTube videos on the problem.

It's a really easy repair, and I managed to pick up "new" ignition coils at the junk yard and haven't had it stall/hesitate since. My guess is that the ignition coils had just started to fail - enough to cause the hesitation/stall but not enough to trigger the code.

I appreciate everyone trying to help!
 

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