Ford 4000 diesel won't run above idle speed

Helping friend with his 1975 Ford 4000 diesel tractor.
Fuel that had water in it was added to tank. Problem was discovered and corrected before engine was started.
Fuel system was drained, all lines cleared out, refilled and everything primed. No air and/or water noticed from bleed screw and all fuel valves open.
Engine won"t start without a touch of ether even when warm. When it finally starts, it would only run at idle speed no matter what the throttle level control was at. During multiple start attempts, it would idle, sometimes speeding up a bit and then slowing down, sometimes appearing to misfire but most of the time at a steady speed. Injector lines cracked open at cylinder head whilst engine running, all 3 are working. The last idling it did was about for 10 minutes, then the engine slowed and stopped as if shutdown lever was pulled. CAV injector pump was rebuilt one year ago and no problems up to this point. I loosened a bolt at the bottom of the pump and a few drops of water came out along with fuel. Doing this did not help much. Could there still be water in bottom of injector pump? If so, do we have to remove pump to flush it clean? Or, could the small amount of water in pump corroded parts inside causing the problem?
It"s something in pump I"m sure, just not sure if water still inside or corrosion damage from sitting in there a few days.

I think there should be oil in that sump if it is inline pump.

Sounds like the metering valve is hanging up - quite common in those CAV rotary pumps. If you know what you're doing, popping the top cover off to free up the valve is not hard.

What did you bugger with on the bottom of the pump? The 3/4" head cap screw on the advance piston? Until you said that I was going to suggest you drain the tank, remove the inlet strainer and clean it, then change the filter again. Now I'm not so sure...
I still suspect it's a supply issue and think you should rule that out first. Second would be a stuck metering valve... but usually you can't make them run if that's stuck.

Rod

If it's really a 4000, it should be a rotary pump.

Check to be sure the fuel return line and pump fitting aren't plugged and fuel is returning to tank while engine is running.

You don't mention changing the filter. A filter can absorb water not allowing fuel through.