Curiouser and curiouser! Randall, any feel for how similar or dissimilar a TR3A engine and a TR4 engine might be? I'm thinking about those occasions when one needs to order parts from Moss or others.
The cylinder block itself is identical, so no worries there. The differences would be in other items, like carbs, starter, flywheel and so on. For example, your TR3A would have originally had the banjo fuel fittings to the carbs; but the TR4 would have had push-on fittings. Pretty obvious, though, so not likely to be a problem. Your pre-50K TR3A would have had the early flywheel with the bolt-on ring gear, which mates to the early, enclosed drive starter. The TR4 would have had the later flywheel with the pressed-on ring gear, which mates to the open drive starter. Hard to say which was installed, probably depends on which gearbox they used. (The gearbox bell housing was modified to clear the open drive starter.)
But all those things might have gotten mixed up anyway over the years; so I wouldn't say the mis-matched engine number really means you have to be more careful. "They're all the same" was a common mantra at the parts store back then, but they weren't all the same and a lot of "wrong" parts got installed because that was what was available. For example, the generator changed in late 59, but the later generator was commonly sold to fit the early cars (probably still is).
All of the common tune-up stuff is interchangeable, so no worries there. (Plugs, points, condenser, cap, wires, and so on.)