I still have the original Sea Scout on Sandpiper (hull #37), and I couldn't be happier with the reliability and smoothness of the old engine. It was rebuilt in 2004, and ran sporadically when I first got it. While troubleshooting I discovered that the needle valve in the carb float bowl would stick intermittently, and I found it cheaper and easier to just replace the whole carb than buy a rebuild kit. I got the carb from graymarineparts.com,, but I'm not sure they always have them in stock. The thing that really turned the engine around for me was when I replaced the conventional ignition system with a breakerless ignition system from www.vannessengineering.com. I had read about Atomic 4's having ignition problems that people would solve by wiping off the inside of the distributor cap, and in every case a solid state ignition solved the problem. I highly recommend making this change, as it will probably save you a lot of grief. Van Ness is a great source for parts and information, and although it is a small company (and it's sometimes difficult to get immediate call backs, etc.) they're very helpful. The owner (whose name I don't recall) stayed on the phone with me for 40 minutes while I struggled to dial in the ignition timing.
One additional caution, the original engine-driven fuel pump on Sea Scouts has a rubber diaphragm and vents through a hole in the bottom of the pump. If the diaphragm fails, the fuel can drain from the tank through the vent hole, filling the bilge. It's a good thing to keep an eye on, and Van Ness can provide rebuilt pumps for a little peace of mind (particularly if there's any risk of introducing ethanol into the fuel system.)
Good luck. My engine runs starts immediately, runs flawlessly, and is incredibly smooth and fuel efficient.