If it hasn't been done, do a CASE relearn with a capable scanner after having changed the crank sensor. Quick relearn to rule it out for your misfire code.
Also, what do all the fuel trims look like when it's running good, and then when it's running rough?
How does the intake air temp compare when it's acting up?
What's the MAF reading in g/s at idle?
The intake air temp started at 80 and gradually climbed to 91 as the vehicle warmed up. I didn't see any crazy fluctuations.
Unfortunately my cheapo scan tool don't provide MAF data. I had basically eliminated the MAF as the issue because my understanding is that it should just read the fuel maps with the MAF unplugged and should run basically fine, just a little rich. In my case it runs just as horribly with or without the MAF plugged in. Am I wrong in thinking this?
It does give MAP data, which was 5.9 cold and 5.0 hot. Once again no crazy readings, just a linear drop as it warmed and idle rpm decreased.
I also sprayed around the intake as others mentioned and didn't see any rpm fluctuation.
One other thing I did notice... In the past, once it's started acting up it begins to pull timing like I'd expect, from it's normal 18-20 degrees down to 12 or so. This time it initially pulled timing, but then I saw it go to 28 at one point and it was knocking hard enough that I was worried about it damaging itself and I just killed it. The rpm signal seemed to be reasonable and not erratic during all this.
Also I should have mentioned this at the beginning but it slipped my mind. When swapping the coils I thought at one point it might be fixed. It had warmed up and was running fine. I slammed the hood and it started running rough again. This led me to consider the wiring, but it all looks fine. Some of the plastic sleeve junk is broke up, but there is no damage to any of the wires as far as I can tell. I also ran a temporary ground straight from the head to the negative terminal and this made no difference.
Thanks to all yall for the input thus far.