Thanks guys fort he help. Yes, the filter does seem like a distribution point...hence my confusion! I do believe the injector is all mechanical. I'm going to try to find the old filter base and see...I'm thinking that the pinhole in the union bolt on the new filter is too small (since the new one is MUCH bigger) and this is somehow messing with the fuel pressure/etc.
The high rev problem probably indicates that the engine is getting enough fuel to rev that high, at least under no load. As far as I know when filters plug up restricting fuel flow the engine slows or stops, not running away?
Has there been any changes to the crankcase breathing system? Maybe some where along the line crankcase vapors are condensing and are being dragged into the air flow stream? If possible, you could temporarily disconnect the breather tube from the intake and see if that solves the high rev problem,
but I think that may be a stretch. I still suspect the injector pump. My experience was with Bosch pumps and IIRC if you remove the pump mark the pump flange and the block so it goes back in the same place. To re-set the timing I needed a timing tool. Maybe Westerbeke has a "help" line or something similar?