You might want to adjust the track bar to create more space between the bolt and tie rod. Also, try checking the alignment again, even though the tie rod length is the same. It could help clear up any issues with toe-in/out affecting steering. You might want to look into a different diff cover...
You’ll need a pilot bushing with a 1” ID to fit the 4.0 crankshaft. You can use a 4.0-specific bushing or a conversion bushing for the 258 to fit the 727 torque converter.
Check the wiring and connections to Cylinder 6, as the inconsistent noid light could indicate an issue there. It might be a wiring fault or an intermittent injector/coil problem.