Timing is controlled by the computer. What needs to be set is the sync signal, and that can be set using a more advanced scanner. Turning the distributor not using a scanner will result in poor running vehicle. The marks on the balncer don't really mean alot like an old school engine with a timing light.

Also, a worn timing chain and distributor drive bushing will make the sync signal be off. I would also look at your plugs/wires/cap and rotor. Look into replacing them if they have age on them. I use factory Champion plugs I get from the auto parts store, but I buy the tune up kit from Mopar. These are pretty basic motors that don't usually require alot other than normal maintance.