Did you replace the injectors while you were in there ???
Plus all the other things mentioned "Grounds, Moving wires around, etc"
Any time I do an O'Haul on one of these engine that has a buttload of miles, I always replace the wiring harness that lays in the engine valley.
WHY you ask???? Well its a bitch to do if not impossible with the manifold on and these wires lay inside a large wrinkle wrap "Loom"
The stuff can and does get crudded up over time with oil residue and other stuff.
These wires move and wiggle some due to engine vibration. They are also subject to lots of heat too.
The connectors that feed the various sensors and the IP get hard and many times the retaining clips break off when you go to remove them.
Wire insulation can and does chaffe through due to contact with the inside ridges of the "LOOM"
Contacts that have been removed and replaced can restore a connection that was getting "Hinky" due to corrosion.
There are all sorts of reasons that a fishbite could go away.
Mechanically there is not too much to look at. The cracks in and of themselves will probably not cause anything you would ever notice.
The cooling system pressurising will cause issues but not an intermitent "fishbite"
A bad injector can certainly cause a cylinder to fire poorly and create a "Miss" or fishbite symptom.
My first thought are that there was an electrical issue with a plug, sensor (Optical) or the PMD and IP connections.
Another cause of fishbite can be the safety bypass valve in the fuel tank.
Now this little beast is located above the suction pickup sock in the tank.
There is a little check valve that will allow fuel to enter the full line should the sock become plugged.
If the fishbite occurs only when the tank level is about 1/4 or less then this is a Red flag that your sock is bad and or the safety valve is leaking.
Air leaking by the valve will entrain in the fuel stream and when it passes into the Injection system, things get real Hinky real quick.
I had these symptoms with DaHoooley over a year and a half ago.
One night I was rolling along and romped the beast to pass and all of a sudden it started bucking and fishbiting then all was well.
Hmmm Plenty of fuel 1/4 tank fresh filter recently ??????????/
Run the rig home and the next day changes the filter harness on the IP, the PMD and the lift pump.
Felt good that the issue would not return.
WRONG later that day I swung onto the main street in town and romped it to get up to speed and poof, fishbite was back with a vengence.
Decided to head home and do some more checking. Stopped and filled the fuel tank as it was now down below 1/4 tank
PROBLEM GONE
Hmmmm just gone
run the truck for a week or so and run the fuel level back down and there was the little gremlin again. Refilled the tank and no more gremlin.
Now even if your issue is not related to a low tank level it can still be entrained air in the system.
If it returns, isntall a clear hose from the IP return fitting up past the wiper on the Drivers side and then back to the return line.
When the FB occurs watch for bubbles in the fuel stream.
Got Bubbles, got a leak on the suction side of the Lift Pump you do.
Have fun, good luck and keep us posted.
MGW