Status update -
To touch base on the O/D issue, I think I was in the final gear, hence it not shifting. If I'm stopped and turn O/D off, the car shifts through normally. Is gear 6 O/D? Sorry, not really familiar with O/D, this would be my first vehicle with it.
I tested out the driverside VCT solenoid and the RPM surge/shudder was still there.
I went ahead and dumped 2/3 of a can of Seafoam into the gas tank. I think I'll let the tank get down pretty low and just dump the rest for good measure. And I don't think this is directly related to this (I think it's related to the COP change), my fuel economy is now averaging around 17mpg. I'd like to try the Seafoam into the intake or whatever, but I'm not quite sure how you get Seafoam to go from a liquid in a can, to being sprayed into the intake. I'll need to find some YouTube videos.
I decided to pull the 4x4 fuse (#23 I believe) just to give that a try. Somehow my 4x4 was still working... what the? No error on the dash or anything. I'll need to further look into this.
I siliconed the crap out of the clips to prevent water from dripping onto #8 and the rest of the engine bay. I didn't realize that there are foam type gaskets between the cowl and the metal of the car right where the clips go in. After squirting all that silicone in and around there, I realized the silicone was dissolving the foam gasket. So I either made the problem worse or better... I guess we will see. I decided to do this to all the clips just for good measure.
I'm starting to wonder if maybe either a new plug or maybe even a new COP that I installed was bad from the factory. Spring Carlisle is coming up next weekend so I'm going to try and find a OBDII to USB cable there. I downloaded FORscan (a free Ford and Mazda scanner program) for my laptop and I am hoping to be able to hook it up, test drive, and find out what's going on in there. I have no idea how to use FORscan, but I'll try to figure it out.
Another thing I'm going to try is to go buy some electrical cleaner spray, disconnect battery, pull the 3 wire harnesses from the PCM, check for corrosion, spray the crap out of the male and female end of the wire harness.
One more thought that crossed my mind, could a bad enough exhaust manifold leak cause a lack of back pressure in the exhaust for that driving range to cause RPM surge issues?