erratic engine problem, water damage?

[JGrant3]

Ok, I have 2006 dodge 2500 5.9. The other day I went and filled up at a farm tank and after about 80 miles of the truck running fine, it started to run very strange. It won't start without a slight shot of ether. When started It seems to idle ok but a little erratic and if you give it a little gas, seems to lose control and run up to about 2500 rpm and miss with a tapping noise. It then gets higher and higher until you are forced to shut it off. I drained and replaced the fuel and filter and I think I got a bunch of water in there. There was a high percentage drained out of the fuel filter but no WIF light.

The next day I put a scan tool on there and discovered that If I shut down cylinder #4 the tapping goes away and it seems to be able to control itself and come back down to idle. I have access to another injection pump, and I am looking at pulling all the injectors and having them tested for damage. Each injector when shut off makes the truck act a little different, so I am thinking they may all be damaged to some degree.

How likely is it that I messed up the injection high pressure pump? What goes first in the case of water? injectors or pump?

I put the spare pump on there and am looking at the same running characteristics from the truck with a good pump. Is there anything else I need to replace or check in the case of water? My rail pressure sensor appears to be working so far.

Thanks for any help, this is looking to be a costly lesson and I want to minimize the blow.