= Solution
The two descendant branches of an equal-rate <Jukes-Cantor model> compose to a single branch of duration $2T$. More explicitly, the model is symmetric, so summing over the ancestral base gives $\sum_a\pi_aP_{ai}(T)P_{aj}(T)$ and a total mismatch probability $\tfrac34(1-e^{-2\mu T})$. Thus use the pairwise difference fraction directly with $t=2T$, rather than halving the differences and correcting the halves separately:
$$
\begin{aligned}
\widehat\mu
&=-\frac{\ln(1-4\times0.29/3)}{29\times10^6}\\
&=\boxed{1.68568\times10^{-8}\ \text{year}^{-1}}.
\end{aligned}
$$
This is the parameter in the printed formula of (c). For a <mutation rate> measured as actual changes per site per year, the conversion derived in (b) gives
$$
\boxed{\widehat r=\frac34\widehat\mu=1.26426\times10^{-8}\ \text{site}^{-1}\text{year}^{-1}}.
$$
The latter is directly comparable to the naive estimate in (a): allowing repeated changes raises that estimate by about $26.4\%$. The exponent parameter and actual event rate are two conventions for the same fitted process, not two different biological estimates.
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