john baez said:
In short, the electric field is ‘infinite’, or undefined, at the particle’s location. So, it is unclear how to define the ‘self-force’ exerted by the particle’s own electric field on itself.
Indeed! It also means the Poynting theorem is invalid at the points where the particles are (it still holds in between them).
This makes its interpretation as a work-energy theorem invalid. It is thus impossible to infer anything about energy from the Poynting theorem.
In relativistic electrodynamics, the electric field has energy density equal to ##\frac{\epsilon_0}{2}|E|^2##.
That is true, but only for regular source distributions, i.e. in macroscopic theory. For point particles, there is no reason to think EM energy is given by this formula. If we use it anyway, we can get anything. The examples you gave and other well-known problems are a result of ignoring this basic problem.
Theory of point particles is not necessarily limit of theory of regular continuous charge distributions (ironically the latter is even more difficult than the former). Point particles have consistent relativistic theory free of the above-mentioned 'self-force' and the original Poynting theorem does not play any role, as it is not valid where the particles are. There is a different theorem of similar significance, which however expresses energy as multi-linear function of individual fields of particles, instead of quadratic function of one field.
Cf.
J. Frenkel,
Zur Elektrodynamik punktfoermiger Elektronen, Zeits. f. Phys., 32, (1925), p. 518-534. (in German, the first paper I know that gives consistent theory of point particles)
http://dx.doi.org/10.1007/BF01331692R. C. Stabler,
A Possible Modification of Classical Electrodynamics, Physics Letters, 8, 3, (1964), p. 185-187. (in English, shorter but presents the same core idea)
http://dx.doi.org/10.1016/S0031-9163(64)91989-4