Shifter seems to have shifted

05 Chrysler pacifica is a 4 speed automatic, next time buy a car with a 5 speed automatic

They probely need adjusted but if you bought it new and it started that go back to the dealer have them fix it .

has the shifter linkage broken?

does it lock up in any gear? sounds like blocking rings trying to stick, what type oil did you put in it?
should take auto transmission fluid

last time i heard of something like that someone stole the driveshaft. in any case you'll have to get a look underneath,

Hi:
The shift pattern is pretty much the same on all 5 speed cars. The top row is the odd numbers, 1-3-5
the bottom row is 2-4-Reverse. The center position is neutral

Here is the key: The shifter is slightly spring-loaded to the center position. If you hold in the clutch pedal and pull the shifter to neutral, and let go of it, it will automatically be lined up in the position, that if you pushed it forward , it would go to 3rd gear, and if you pulled it back, it would go into 4th gear.
This way, to start driving, you start out in neutral, grab the shifter lightly, and push it first to the left, then forward. This is first gear, where you start out. when you want to shift to second, push in the clutch, and keeping left pressure on the shifter, pull all the way back . Here is the easy part, 2nd to 3rd. When you are ready, push in the clutch, and just push the gear shift forward , till it hits neutral, and is spring loaded to the middle. Then you just push it straight forward to 3rd, then next shift, straight back to 4th.
Last gear, 5th: push forward to the neutral row, then Push to the right till it lines up ,and forward to the 5th gear. Reverse should only be shifted into from a dead stop. Find neutral, push the shifter all the way right, then pull back towards you. Hope this helps.
Practice a bunch in the driveway!

sounds like the shifter linkage has worn and not working properly need to lift in air and inspect the linkage

syncro problem
low on oil
check stick shift adjustments
shift stick bushes or a cable problem
check engine mounts
gearbox, fork or clutch worn

If you can see where the shifter goes through the floorboard, make sure the shifter is not hitting the floor.
There could be interfierence under the car also.

Grinding going into third gear only may indicate a worn syncronizer ring. There are no adjustments on the shift cables, so I doubt highly that changing the cables will help you, since you are talking about 3rd gear only. Please note: This issue may be still under warranty, if your vehicle has less than 60,000 miles and is not 5 years old. Replacement of 6-speed internal parts is best left to a pro.