I have water coming into the passenger side after a rain when this happens the car wont start. I can jump it and as long as it is not raining the car runs great! I have had the battery checked, alternator good, so not sure what the problem is. Any help would be greatly appreciated!

 

Common problem. Your cowl drain is plugged (should be able to find lots of threads on it). Clean it out, then you will need to check the smart junction box in the passenger inside kick panel. Make sure it hasn't been damaged or connections corroded. That will cause a lot of problems.

And you probably need to pull the carpet back and dry that area well.