Here is how to MAKE SURE the distributor is indexed PROPERLY on a 4.0
1-Remove distributor and remove the distributor cap, cam sensor and rotor button
2- Remove #1 spark plug
3-rotate engine by hand until you feel compression coming out of the spark plug hole (3/4" or 19mm wrench on crank pulley)
4-continue to rotate until the timing mark on the harmonic balancer (crankshaft pulley) lines up with the "0" mark on the timing cover
5-Locate the hole on the bottom of the distributor housing. There is also a corresponding hole on the plate that spins inside the distributor housing. Line them up and drop a pin (screwdriver, drill bit, etc) into them. Now the distributor and pickup plate are indexed properly.
6-With a flat head screwdriver, rotate the oil pump (through the hole where the distributor sits) to approx the 11 o'clock position
7- With the pin still inserted in the distributor body, drop the distributor into the engine block. Do not remove the pin if it doesn't drop all the way in the first time. Rather, move the oil pump drive a little
8-When the distributor is fully seated and the retaining hole is lined up, remove the pin and bolt the distributor down to the block.
You are now timed/synced/indexed properly. Period.