Joe - thanks for the comments. Here are some responses to your questions:
Compression - I didn't check it, because I really haven't had a problem with power or burning oil. Even though the engine is 25 years old, the number of hours we put on these engines is negligible compared to a stink pot.
High Pressure Injection Pump - all I did was flush it and replace the seals. Kept the same number of shims (original) under the case so as not to change the timing.
Flushing your Yanmar - I used a hammer, chisel and Dremel tool and blew the chips out with an air hose to remove significant scale in the water passages before reassembly and flushing. Depending on the age and amount of scale you have, you may want to use a much stronger acid (Muriatic) if you are not disassembling and mechanically removing the scale. The other way to approach this is leave your engine in the boat but remove the heads. I found most of the scale buildup in the upper section (heads, water manifold that holds thermostat, aft zinc holder). These can be taken home and cleaned on a workbench. The block can be cleaned in place, although my basement was much easier to work in than cricking my neck on the boat.
Bill