When it starts to miss, does it spit white smoke out the exhaust? If so, it's definitely an advance issue, as Al said. Manually advancing the timing as Al described will confirm the problem if it goes away once you do that. Pull the top of the pump toward you to advance. Best solution then is to remove the pump and have a pump shop free up and/or repair the advance mechanism.
If it does NOT spit out white smoke during the miss, and if it only does this under no load (meaning it runs and sounds fine under load), then I would simply call this a "minor irritating flutter" and ignore it myself. Yours wouldn't be the first 3 cylinder Ford tractor that did that.
Disclaimer: The advice above is governed based on what I *think* it sounds like, not necessarily what it actually sounds like. A YouTube video of the problem could be very helpful here.