Hi,
Gotta make some waves here playing devil's advocate and having had both. It's just not that simple
The Atomic 4 is much quieter. There is nothing inherently wrong with the reliability of the Atomic 4 compared to a diesel, and one could very easily argue that the diesel has a much more complex fuel system requiring injection which can be ruined by even the tiniest amount of dirt in your fuel. The A4 uses one of the simplest most reliable fuel systems in the world - a carburetor. Start looking around at all the posts on folks who changed their diesel fuel filter and couldn't get it to run again because of prime problems.
Diesels operate at a much higher compression ratio (like 20:1 instead of 8:1), so the load a diesel handles internally is much higher than the A4. Better do your oil changes and maintenance on the diesel (just like the A4). Neither the A4 or a properly maintained diesel should have any issues of catastrophic failure e.g. throwing a rod.
Regardless of the power plant in your boat, if you carry any fuel source e.g. alcohol for a stove, gas for a dinghy, propane etc., you better run your blowers and go through the same safety drill you do on a gas powered boat. While it is very rare, there has actually been documented a case where a diesel caused another fuel source to explode on starting.
Bottom line, if your boat is already powered by an Atomic 4, unless you just have a bunch of money to spend (like $5K-$10K), and really need long range cruising under power, I'd highly recommend keeping (or fixing) the Atomic 4. I have found running A4s for as little as $500 ready to drop in and use. I am just finishing a full rebuild on one, and we're coming in under $1K for all parts and machine work. I can assure you there is no drop in replacement other than the original engine, and you need to be prepared to work on everything from stringers and cuttig holes in bulkheads, to playing with your prop if you switch from the A4 to the diesel.
So, diesels are noisier, get better mileage, don't have as dangerous a fuel source. A4's are simpler, smoother, quieter. Tough choice, honestly. My own quandry is that I have an under powered diesel (Yanmar 2QM15 - 2 cyl/15hp) in my Independence 31 (12K displacement with extra ballast), and have a nice powerful A4 sitting in my garage. If it weren't for the fact that I know what a pain switching from one physical engine layout to another layout is, I'd drop the A4 in and get the power I want. However, I don't feel like the hastle of reworking stringers, a new fuel system, etc., so for now, I'll do another year with the tiny diesel, and may end up selling the A4.
A final thought. I think the biggest plus for a diesel that has not been mentioned is it's ability to run without electricity. This has more appeal to me than any other aspect. I am more worried about being on an extended cruise and having an electrical problem e.g. something is left on, the battery switch was left on "both" and you wake up one morning to stone dead batteries. With the diesel, if you are set with a hand crank, you should be able to get it running, charge batteries etc. Another of my paranoid scenarios would be the lightning strike that blows out the electronics on the boat, but the little diesel might just still run and get me where I need to go....
Good luck on your project. Don't be scared of your A4,and if you do the switch to a diesel, keep us posted on how it goes and what you think when all done.
-David
Independence 31
Emerald