Here's a couple of thoughts. I had the same problem on my Yanmar 2GM. I pulled the pump off and took it apart. Since the pump doesn't have any rebuild kit, and was going to cost around $80, I decided to look at it myself and see what I could do. Once apart, I determined that the diaphragm was still intact, and was not the culprit. I took out te two check valves that let the fuel flow in the proper directions. Under one was a small fiber washer it was not seated properly and well worn. I couldn't buy the part from any Yanmar dealer, so I went to Ace Hardware and found some tiny O-rings. I replaced the washer on the bottom of one chck valve, and one on the top of the other check valve. I put everything back together and submersed the pump completely in fuel. While immersed, plug up the fuel outlet with your finger and pump the rocker arm that rests on the cam and actuates the pump. If you see any bubbles coming out anywhere, you have a leak. Mine had a small leak coming out by the diaphragm. I took it apart again and checked the diaphragm and the pump housing for any imperfections. The diaphragm had a little area that looked like a buildup of gasket sealant or something. The housing had a slight pitting of the casting. in the same area. I took a small scraper and carefully scraped the gunk off the diaphragm. Then I sanded the casting carefully with some 600 grit wet sanding paper with a block backing it, making sure to use full even strokes across the whole casting, and taking off as little as possible. After cleaning everything, putting it all back together, and checking it again, I found that there were no leaks. The total cost of the repair was 43 cents. plus a little diesel fuel. I now have over 100 miles logged, and have had no problems as of yet. (Knock Wood)
I thought about replacing the pump with an electric one, but I learned from a question on the forum, that if my battery is dead, and I need to start my motor, I'm screwed with an electric pump. My motor is small enough to crank by hand if I had to. I might add an electric one as a secondary pump, but I don't like the idea of relying solely on an electric pump.
Dave