1997 nissan pathfinder timing off. I replaced water pump(behind timing belt). Timing "gears" got moved (two top ones). I don't know how to make sure everything is lined back up correctly.Any ideas?

I doubt the problem is timing. If that were the case, it would have the same miss at road speed.
Is the check engine light on ?

You really should have the repair manual to your Terrano(Pathfinder). I recently had to replace my water pump on my 89 Pathfinder, so I went on youtube and watched videos pertaining to the task and took their advise.
It is an easy job, however you should replace the timing belt and thermostat when you do the water pump, The tensioner should be replaced too. Their are certain orders and torch specs to loosen or tighten bolts so You really need the manual. Plus if yours is like mine if you dont get the timing on right then you risk messing up the motor. Hope this helped you out.

Water Pump Removal & Installation To Remove:

1. Allow the engine to cool and drain the coolant from the radiator and both engine block plugs.
2. Remove the fan shroud and both radiator hoses.
3. Remove the drive belts.
4. Remove the water pump pulley.
5. Remove the crankshaft pulley.
6. Remove the timing belt covers.
7. Remove the water pump.

Water pump removal/installation

To Install:

1. Install the water pump with new gasket.
2. Install the timing belt covers.
3. Install the crankshaft pulley.
4. Install the water pump pulley.
5. Install the drive belts and fan shroud.
6. Install the radiator hoses.
7. Install the coolant drain plugs.
8. Refill the cooling system.

the marks for th cams are on the tin stuff behind the gears study it for a bit and nyoull see them the mark for the crank pully is on the case onthe bottom of the crank pully just of to one side

yes you will have to remove the timing belt and crank pully. It is not as bad as it looks. You might as well, while you are in there, change the thermostat and new Timing belt and tensioner pully.
The trick I use, (and I have done hundreds of Timing belts) I use a good paint pen to mark the timing belt and gears. make sure to mark it so you know what marks are for what cam and crank. and which direction it goes. then on the new belt crefully transfer the marks. then it goes really smooth and there is no guessing hoping it is properly lined up on the factory marks. and you dont have to line every thing up before you take off the belt either. just mark it and remove it where the motor stopped..If you do it this way, you dont have to worry about trying to line up the cams and crank to there respective marks, just the ones you made, then there is no mistake.

My apologies for the delayed response. I am going back and answering questions that were never answered.
Click on the following Link. It has all the Diagrams for the Timing Belt you will need.
Before Clicking, let me know if this helped.
Again my sincerest apologies...

http://www.2carpros.com/car_repair_information/year/1996/make/nissan/model/pathfinder/1996_nissan_pathfinder_timing_belt_diagram_marks.htm

If it ran fine before and you did not move the distributor (if it has one), then you must not have gotten the timing marks aligned properly on the crank and cam pulleys. If that is the case, unfortunately you will have to take the timing cover back off and get the belt installed with the pulleys in the correct positions. This link provides information on what the marks look like and why this is the only way to fix your problem.

need to remove belts/fan timing cover /rotate tdc aling marks /remove damper pulley/remove second timing cover/ remove water pump

The water pump is located behind the timing chain cover. There are two black plates on the front cover. The one near the front of the car has the water pump behind it. The other one has the timing chain tensioner behind it. First you must drain the coolant. Then support engine and remove engine mount. Then remove drive belts. Then remove the two black plates. Push the tensioner in and lock it with a paper clip. Then remove the two bolts holding the tensioner and remove tensioner. Then remove the water pump bolts. Rotate engine crankshaft the take tension off of water pump (about 20 degrees). Then install two bolts into water pump threaded flange (M8). Tighten M8 evenly as water pump will come without damaging it. Check for corrosion. Then replace with new one. Make sure you use new "O" rings. Lubricate with engine oil. Put the original three bolts back in the water pump. Then install timing chain tensioner and black covers. Replace belts and engine mounts. Add coolant and pressure test system.

Simply buy a new belt from Nissan. Line up the marks on the belt with the marks on the cam gears and crank gear and it will start.