I am working on a 650 komatsu, we had a batch of bad fuel delivered few weeks ago. Emulsified water!!! Drained the tank on the 650 and put 30-40 gallons of good fuel in it and drained it again! It did run before we seen the fuel problem! About five mins and plugged the primary and secondary filters! Sence then I have changed 10-15 filters. Finally got filters to stay clean but is is constantly running filters dry and dying. Fill them up pump the primer, fires right back up! Now we are noticing if it is under half a tank it really has hard time, also if going down hill (steep) it dyes every time! Did we kill the pump...it runs fine up Untill running filters dry, so what about the lift pump? Check vale maybe but that shouldn't matter while running I wouldn't think! Even checked vent on fuel cap. Any thoughts would be helpful.
Pull the fuel gauge/ pick up assembly and examine the pick up. A loose connection or cracked hose or tube would cause the symptoms you describe..
I'll second joispoi, if you plugged that many filters there was a whole lot more in that bad fuel than just water. You've got an air leak if there's air in the filters, but that's probably caused by a plugged up screen or tube.
There is a fuel strainer on this rig that plugs when you get grit. On the older models you had to trace the line from the tank to the strainer to find it. There is a good size basket strainer inside the cast can.