All right so here is an update after talking to the mechanic: the clogging theory is definitely possible especially if the filter hasn't been changed in a looong time (mine hadn't been changed in 12 years). However, I changed the filter again just for the heck of it, and absolutely no sediment flowed out of the filter--only clean gas. So in this case, that was not the issue. Now here is the big thing: Keep in mind that the guy I went to worked for a Chrysler dealership for 20 years specializing in diagnostics. Currently, he is a one-man-crew, independent shop. He knows his stuff and is one of the most honest mechanics I have ever met (I mean, he spent an hour+ on the phone with me just trying to trouble shoot and telling me his experiences with this type of thing) Unbeknownst to me, my neighbor has recommended that guy to a lot of people.
The problem lies (once again!) in the PCM. I thought that was taken care of since it was replaced not too long ago, but that is not the case. He told me that PCM problem in the 96 ZJ's were about the worse and the 97's only got a little bit better. He still to this day doesn't know the problem nor does Chrysler really know. Whenever they came across this "PCM" problem at the dealership, they put a new one in and sometimes saw within a day, a month, or whatever that same car come back in and the computer code for the "bad PCM" would pop up. (When he ran the scan on my system the PCM code was the one that came up many times).
Here's the crazy part. When they sent these "Bad PCM's" back to be tested for a bad resistor or something wacky in the computer board, almost all of those "Bad PCM's" were sent back to them with a guarantee from the testers that there was nothing wrong with the computer board. No bad resistors, shorts, nothing. His only theory was that the way the pin connectors aligned was a possible issue, but they did everything to make sure those were secure (adding dielectric grease etc). He did say that with some models the entire problem was that water was getting into the pin connections and you could tell because there would be like water stains in the connector area. (I forgot which models he said though.)
Anyways, when he was telling me his theories, that sparked my memory of a website I came across a long time ago when this problem was happening. It's www.dyingjeep.com
I have taken a gamble for $20 bucks to see if their proposed fix actually fixes it. I was kinda like, "either $475 for a new PCM, or $20?" Luckily, they accept paypal so, being a security freak like I am, I was comfortable with that. If all else fails, I'm out $20. If it was a scam, paypal would fight it for me. So I installed their mod last night and even added my own mod. I drove the car today fairly hard (sped up then quick slow downs, hardder stops, idling for a long time), and Thank the Lord, not even so much as a sputter. We'll see what happens this next week and if this really is the fix. Even if this mod doesn't fix the problem, these guys seem to be on the right tract entirely to which I will investigate further until I have the absolute answer. The mechanic was very intrigued by their theory and wants me to keep him updated too. If it doesn't work, he and I are going to pull apart that pcm. Since I didn't find the answer myself and dyingJeep.com is charging for it, it would be entirely unfair to reveal their findings on this forum. If it works though, I will with 100% confidence condone dyingjeep.com and let you all know that $20 is entirely worth it.