  We present new methods to minimize the systematic and random errors for
measuring the transmission power spectrum from the Lyman-alpha forest. Sources
of systematic errors explored include metal line contamination and
continuum-fitting. We advocate the technique of trend-removal in place of
traditional continuum-fitting -- here, a spectrum is normalized by its
(smoothly varying) mean rather than its continuum -- this method is easily
automated and removes biases introduced by continuum-fitting. Trend- removal
can be easily applied to spectra where continuum-fitting is difficult, such as
when the resolution or signal-to-noise is low, or for spectra at high
redshifts. Furthermore, a measurement of the continuum power spectrum using
trend-removal, from either low redshift quasar spectra or the red-side of
Lyman-alpha, allows in principle the removal of spurious power introduced by
the continuum and thereby expanding scales probed to larger ones. We also
derive expressions for the shot-noise bias and variance of the power spectrum
estimate, taking into account the non-Poissonian nature of the shot-noise and
the non-Gaussianity of the cosmic fluctuations. An appropriate minimum variance
weighting of the data is given. Finally, we give practical suggestions on
observing strategy: the desired resolution and S/N for different purposes, and
how to distribute one's finite observing time among quasar targets. Also
discussed is the quasar spectroscopic study of the Sloan Digital Sky Survey,
which has the potential to measure the power spectrum at z ~ 2-4 accurate to
better than 1 % per mode -- the techniques presented here will be useful for
tackling the anticipated issues of shot-noise and continuum contamination.
