Jeger wrote:
I am considering adding a prefilter/water seperator to my CRD as well. What I want to know is...What happens if the stock filter was to get clogged or the pick up line blocked of or a line pinched etc. Does the current setup have some sort of system to detect this condition? If it does then we may not need to worry so much about hurting our pumps. So does anyone know?
What happens is the bloody engine just quits running as you're going down the road at 60 mph!!!

Been there, done that, not just once but twice. Also has a tendency to cause a strange stain on the seat when this occurs.
It will throw a code, P0093 Contaminated Fuel, based on the difference of actual versus programmed fuel rail pressure. But from my experience, by the time it's clogged enough to throw this code, just shifting from Park to Drive is enough to kill the engine.
First indication that you're getiing a clogged/water soaked fuel filter is none other than the infamous tranny two step, the ye olde buck and jerk at certain speeds and throttle conditions.
Next stage of progression is you're cruising happily down the road steady state, and come upon an incline or other situation that calls for a moderate increase in engine speed/throttle. After a few seconds of this increased fuel demand, the engine sputters and flat out quits. You're able to restart and continue on your way, but find out that above a certain RPM the engine is starved for fuel and dies again.
The condition gets progressively worse, the RPM and load at which the engine will continue to run getting progressively lower, until even just putting it in drive is enough to kill the engine and finally throw a CEL.
The factory filter is 3 micron. When I was running with just this filter, every time I checked it, I never got any visible water out of it, even after several tanks. I believe RFCRD is correct, this is a wick type filter that absorbs the water instead of separating it out, and by the time it accumulates enough to give you the "Water in Fuel" warning light, it means it's chock full of water already, and you're already long since SOL and stranded at the side of the road.
I added a Permacool Fuel Filter/Water Separator, 2 micron, 24K miles, $50 for a kit, $12 for replacement filter, from JC Whitney. I added it in AHEAD of the factory filter in the engine compartment. I know that sounds backwards, but I'd rather replace a $12 filter first than the $40 factory one. I also mounted it where it's a 5 minute job to change it out, not the PITA evolution required for the factory filter.
Every time I've drained down the Permacool filter (old style petcock on the bottom), even after just one tank, I've ALWAYS gotten some amount of visible water out of it. Couple of times I also got gray/brown sludge along with the water, which indicated microbes, and I double dosed the tank with biocide for a while until this went away.
I just did a drain on the filter this morning. It'd been about 2 months, 4 tanks, since the last time I'd checked it. The last few days the beast had been trying to do the buck and jerk routine at different times when driving to work, which told me it was due. I drained out nearly 2 ounces of water and some visible chunkies. After repriming the system, it purred like a kitten on the way to work, not a hint of a stutter.
A $50 filter kit is cheap insurance compared to what a set of injectors and a fuel pump will cost you. This to remember as well - PROBLEMS DUE TO CONTAMINATED FUEL ARE NOT COVERED UNDER WARRANTY, YOU EAT THE COST OF REPAIRS!!!!!! In my case I was lucky, all that was required was a drain and flush of the fuel system, but even that ended up costing me $300, plus the cost of a full tank of fuel. If you're smart and save your receipts, you can recover the cost from your fuel supplier.