Things to Check- Spark plugs, plug wires, coil(s), and crank angle sensor. Here is a good youtube video that will help you diagnose the problem although year and coils are not exactly the same as yours and you probably don't have the testing equipment they do it gives you some good info on what to look for.
https://www.youtube.com/watch?v=xwh3XM1Nl4k
Also just double check all your plugs and grounds to make sure they are in tight and secure and that you did not get any water in them when changing the water pump.