Try this:

Get a plastic milk jug, cut it open so you can wipe it clean with a
rag. Put fuel in it. Get some clear tubing from Lowes or Home Depot.
Run the tubing to the fuel fitting on the inlet to your fuel pump.
Fill the tubing with fuel and allow it to siphon the fuel from the milk
jug. Start your engine. If it does not lose power as it did before,
then suspect your fuel filtration.
The Yanmar mechanical fuel pumps seem to go bad all the time. I got an
electrical pump from JC Whitney that I put in series with the
mechanical one. It is wired to the starter so it always provides low
pressure to the engine. It keeps the engine primed.
It sounds like you have both engine timing and fuel problems. Valve
timing is easy to set on this engine. Injection timing is a little
harder but a COMPETENT mechanic can do it. You can do it yourself if
you can follow the directions in the service manual.

For cold starting, use the decompression levers. Relieve compression
on one or both cylinders, get it turning then put in compression, this
will get things lubed well and moving before you are trying to work
against the compression.

You might also check your fuel return line. If it is blocked, you can
have problems. When you are priming the engine, remove it from the
fitting on the injectors, blow into it (a little diesel fuel in your
moth will not hurt you) to see if it is clear.

Take the exhaust hose off the exhaust manifold and run the exhaust into
a 5 gal bucket This will fill your cabin with smoke so be careful but
the idea is to see if your muffler is clogged..