Can only offer partial suggestions. It does sound like the engine is being starved for fuel. There is a 3rd, small, fuel filter - part of the fuel pump or just up stream- I forget. That would be worth checking into if it's never been changed in a thousand hours.

Also- when you encounter the stumbling engine- can you hear any different sound that the fuel pump is making vs. the pump sound when the engine starts and runs normally?

I had a similar problem a few years ago. We had picked up some fuel with emulsified water in it. The Racor filter does not stop all of it. We could run hours before the engine would run rough or stop. The engine, could be restarted. When I finally determined it was the fuel I pumped out the tank and put in fresh and the problem went away. You might want to see how clear the fuel in you tank looks compared to fresh. The two pictures attached show the difference from the top to bottom of the tank. Fuel was from the Bahamas, no pink.

SeaBird;
 Name (?, Location ?)
We had a similar problem several weeks ago and it drove me bonkers until I located the source of the problem. The engine would run at various RPM and then slow down - then speed up in RPM's .Never quite quit but wild variations in RPM.  We were motor-sailing several miles off shore and more than a little concerned. I followed much the same procedure as yourself, checking the Racor Water Separator Filter for contamination, inspection fuel lines, fuel filters and fuel pumps.
 
After very close inspection, what I found was that the Racor water separation filter assembly was actually at fault. Upon closer inspection of the Racor filter assembly, I found one of the Racor's rubber  'O' rings - located behind the filler nut at the top of the filter assembly  - had actually broken down over the years and caused an air leak in the fuel supply. This air leak was the cause of the varying RPM's issue.  Replacement parts from Racor are difficult to obtain and, since the boat is 20 years old and the filter assembly probably is too, our remedy was to buy and entirely new Racor Filter Assembly. I installed the new filter assembly, including a new filter, and did not see the problem again.
Given some of the more recent comments regarding Racor filters, (paint disintegrating, rubber parts breaking down, etc,) it might be a wise idea to invest in a new water separating filter assembly or look for another brand.
Let us know how you make out.
Bill

Had a similar problem. Kept changing the filters and nothing helped. Finally had a tech check it out an found that the fuel line goes into the water separation filter at a 90 degree angle. The line clogged at that point before the fuel got to the filter. After that was cleaned out, no problems. He had to take the filter unit out and clean it out in the shop but maybe you could disconnect the fuel liner at the filter and try using a pipe cleaner to get the junk out.

Lots of good suggestions here, one to add is check the tank pickup tube. They can get clogged. One way to check is to remove fuel gauge sender and then pull the fuel line into the Racor and blow compressed air into the line back to the tank. It should flow freely. 

Also check tank tank vent for obstructions (insect nests)

As far as the OP switch - you should get a buzz in the key on - with no glow plug power. No buzz with glow plug power.   I never liked that design— too complicated  especially on something as critical as OP.  My M25 never had this type of circuit but I like the result (no buzzer while heating the GP’s so I put in a simple waterproof relay to kill power to the buzzer while the GP’s were energized.  

Les

What you are describing could be a fuel pump cutting out.  I had a broken lead at the pump and the wire was being held in by the zip ties on the wiring harness.  It would cut out just like what you are experiencing. The engine would either shutdown or only run at low RPM.
 
For your second question, Yes.  The techs are known for being off from being from the factory and it easy to check.
 

Erik
The tach is checked by  putting some reflective tape on the flywheel and "shooting" it with an optical tach (the association tool loan program has one - or 20-30 bucks at harbor freight).  The tach is then adjusted via a small hole in the back of the tach and an even smaller straight slot (think bobby pin).  I upgraded to a digital tach and it uses button pushes on the back - a royal PITA.

If you were local I'd loan you mine.

Hi,
it may be that your lift pump is failing.
I had the same problem last year, with the motor starting ok, but then after a while cutting out.
The problem became more frequent and worse.
I replaced the lift pump (whish was dead) with a much better quality one and all is well.

cheers

Hi,
If you take out the fuel guage you can pump out the fuel.
you can then clean out the tank quite effectively by using a cheap wet and dry vacuum cleaner.
 get a piece of thin piece of
dowell and attach a piece of plastic tubing to it. securely tap the end of the plastic tubing tape to the end of the vacuum cleaner hose.
you can then guide to thin hose around the bottom of the tank. you will be surprised what comes out.
I have done this and picked up a lot of gunk and moisture from my tank.
lets know how you go
cheers

Hi Bob,
I used a small electric 12 volt pump.
I was lucky that our Yacht club has fuel and oil disposal tanks.

cheers

Erik, Sounds and looks like you have some very bad fuel there and should find he source of that much water. Inspect the 'O' ring at the deck filler and try and understand where that much water is coming from. Not sure where you are buying your fuel or how long that fuel has been standing. We buy our fuel only at places that pump a large quanity of diesel fuel as water condensates in their tanks too.

On a fuel transfer pump, we cleaned out out fuel tank using this inexpensive pump from Amazon and it worked perfectly to get the 30 gallons fuel out of the tank. (See link below) The remainder of the crud at the bottom was sucked out with a 'wet dry vac' as suggested above. With regard to disposal of oil, we spoke to the fellows that collect our garbage and they said the county would make a special pick up if I called them so I suggest that you call your normal pick up service and ask how you dispose of the oil.
https://www.amazon.com/TeraPump-TRHA01-Battery-Operated-Transfer/dp/B00A...
We've since replaced that pump and use a different pump for transferring fuel while underway.
This is what I am using now to fill from aux. tanks while underway.
https://www.amazon.com/Second-Gen-TERAPUMP-TRFA01-Auto-Stop/dp/B00SBZRKEU/ref=pd_sbs_263_1?_encoding=UTF8&pd_rd_i=B00SBZRKEU&pd_rd_r=89EBATMP6GWNBGJEECH3&pd_rd_w=uwCqJ&pd_rd_wg=tWgw5&psc=1&refRID=89EBATMP6GWNBGJEECH3

TeraPump A-TRFA01-001 TRFA01 2nd Generation Battery Powered Fuel Transfer Pump - 4AA Battery, 3 GPM  (Also at Amazon)

Erik;
Did you dispose of the remainder of old fuel or re-fill it back in to the tank ? Did you change out the Racor Filter Assembly or just the filter ? Did you see any variation in RPM on this last voyage ?
On the slight amount of water in the Racor; That might be a result of water in suspension (emulsification) in your RETURN fuel line although, it would not be very much. (Recall that very little of the fuel that is supplied to the engine -is used by the engine. The majority of the fuel is sent back into the fuel tank via the return line)
If you started with fresh fuel (disposing of the old) and still see significant amounts of water getting into the new Racor filter - check that 'O' ring on the deck fuel filler cause that water is getting in somewhere and it will be a challange to find it. . Rain or condensation can be a problem too. Check the Racor frequently for water and drain it.
Another factor is how often your engine is run. Diesels that are run frequently usually have very little problems with water.
How did you make out with the tack problem ?
Bill
PS. Check your messages here on the board.
 

@seabird you can adjust some of the tachs by inserting a very small straight slot screwdriver (think bobby pin size) into a hole in the back of the tach  - if it’s not linear adjust so it’s right at cruising speed.  

Les

I have a 2002 and the charger is in the seat in front of the gally to the left,looking aft, of the AC unit

Erik;
 Hopefuly you replaced the '0' ring on the fuel filler pipe as well.
 Bill

Erik;
 That's the '0' ring I was thinking about. As I mentioned in an earlier post, my air leak was in the Racor filter housing itself. (Bad '0' ring in the filter assembly) Outside of the fuel tank vent, there should be no other spots for the water to get in. Let's hope the new filters & hose took care of the issue.
Bill

Erik;
Les is right on the money regarding fuel pumps and filter size. We had very much the same confusion when we started with our boat. On a visit to the factory in Largo, FL - we asked Gerry Douglass; 'Why would you put 2 micron fuel filter on the Racor and 10 micron filter on the engine ? Seems it should be the other way around ? His response was interesting; 'Ever tried to change an ENGINE filter in a seaway ? Much easier to change the Racor when under way' (Most Catalina's are equipped this way from the factory)
Now all of this just points to the confusion surrounding the issue. Diesel Guru Nigel Calder says' Use a 30 micron on the water seperator and a 10 on the engine'
But these comments usually do not take into account on how one individual is using his boat or how many gallons of fuel is being run through the engine.
Let me explain. If your diesel is running a continiously operating water lift pump in a farm type application- you might burn 85 gallons of diesel fuel per week in your XP 25. (Based on .5 per hour gallons X 168 hours) and you are buying your fuel from a reputable source like the local truck stop who pumps lots of fuel a day, this fuel might be relatively free of contaminants .  So a 30 micron (Racor) and 10 (engine) will be more than enough.
In contrast, compare that to a guy who uses less than 30 gallons over one or two seasons and is in a place where diesel fuel has sat in the tank for a while. The Islands ? Water and mold will build up and better filtering is required. This is where the confusion starts. All boat use is different and some use the engine more than others.
Your injectors will tolorate a solid item of about <10 microns.
Les makes the point that a 2 micron filter on the Racor primary filter  will cost you a lift/fuel pump and he's right - as it takes considerably more effort (pressure) for that pump to pump fuel through that two micron filter.(So add a fuel pump to your list of spares)
  OK, with all that logic behind you, you are in  marina with reasonabably clean fuel, I'd use a 30 micron on the Racor and a 10 micron on the engine. As Les mentions, the Wix engine mounted filter is a great filter.
Hope that helps.
Bill