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My Yanmar (4JH3-HTE) has been faultless albeit a little smokey of late.
I have never really run it too hard and probably even too gentle for a diesel. So today I decided to run it at almost WOT (3500RPM out of 4000) to see if it was a carbon build up issue. Slowly but surely the smoke reduced to almost nothing. BUT..... when I reduced the power back towards idle, the trusty diesel just stoped.
It would run on successive attempts at idle and on increase of power, but every time the power lever was bought back to idle the engine just stopped. It had also been in the past an instant starter. Now it kicks over after about 3 seconds of cranking.
I am hoping all I have done is somehow thrown out the timing. What are the your thoughts 
My guess is that the high revs dragged a lot of (dirty) fuel through the filter and clogged it.
Try a filter change before you panic.
Just a guess though.
Gary
The consensus thus far seems to be a blocked (or gunky) filter. I haven't had the opportunity to get back up there (work/kids getting in the way). But at least it would be an easy and cheap place to start.
Cheers 
If clearing the filter doesn't work, check for any tiny air leaks in the fuel system. Loose banjo bolt, hardened copper washer, pin-hole in hose, etc are all culprits. This often shows up as loss of power and high revs, but is worth checking as you work through the list of possibilities.
Dodgy lift pump is another possible cause, as is blocked tank breather.
Identical problem with my similar Yanmar. Did a replacement of both filters and checked tank. Turns out tank was lined with black crappy stuff and so was my temporary tank.
All cleaned now and working well
Here's a different thought. Could the throttle cable adjustment be out of whack now that you have almost fully extended it after your WOT. Maybe something slipped. Will it idle if throttle is just moved off idle position.
A good thread. Prompted me to change my primary (is that the correct term for from the tank) on the weekend. It was filthy. Been meaning to switch it for ages but keep putting it off until next week to go sailing instead.
Cleaned my tanks when I first brought my boat and from then on, every drop of diesel that went into them, went through a "Mr Funnel" and then I added in some Diesel Fuel Treatment to (try and) prevent the black death. Also always kept my tanks full. After 10 years I never had one fuel issue and the 2 seperate pre-filter glass bowls were always clear.
I also made my fuel draw point (tube) about 3 mm from the bottom of the keel tank to make sure I wasn't creating my own version of amargeton, that was going to come rocketing through my filters the moment I ran my engine in rough weather. If there was any chance of crap finding its way into my keel tank, it was going to be coming straight back out rather than saving it up for "Murphy' (or Sod) to use at his discretion.
Diesel Engine Basic Rules:
1. Clean Air
2. Clean Fuel
3. Cooling System maintained
4. Oil Changes
5. Never, Never, Never run Unloaded. (An alternator is not enough load. Throw the mooring lines off and go for a run if you want to charge the batteries)
www.mrfunnelaustralia.com.au/buy-online.html
