The radio millisecond pulsar PSR J1023+0038 exhibits complex timing and eclipse behavior. Here we analyze four years worth of radio monitoring observations of this object. We obtain a long-term timing solution, albeit with large residual timing errors as a result of apparent orbital period variations. We also observe variable eclipses when the companion passes near our line of sight, excess dispersion measure near the eclipses and at random orbital phases, and short-term disappearances of signal at random orbital phases. We interpret the eclipses as possibly due to material in the companions magnetosphere supported by magnetic pressure, and the orbital period variations as possibly due to a gravitational quadrupole coupling mechanism. Both of these mechanisms would be the result of magnetic activity in the companion, in conflict with evolutionary models that predict it should be fully convective and hence non-magnetic. We also use our timing data to test for orbital and rotational modulation of the systems $gamma$-ray emission, finding no evidence for orbital modulation and $3.7sigma$ evidence for modulation at the pulsar period. The energetics of the system make it plausible that the $gamma$-ray emission we observe is entirely from the millisecond pulsar itself, but it seems unlikely for these $gamma$-rays to provide the irradiation of the companion, which we attribute instead to X-ray heating from a shock powered by a particle wind.
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