  This dissertation explores two main topics: 1) Color Transparency and
quasi-elastic knockout reactions involving pions and $\rho$ mesons; and 2)
determination of the $J/\psi$-nucleon scattering amplitude and scattering
length via $J/\psi$ electroproduction on the deuteron. It is shown that at the
energies available at the COMPASS experiment at CERN, Color Transparency should
be detectable in the reaction $\pi+A\to \pi+p+(A-1)^*$ (proton knockout). It is
also shown that Color Transparency should be detectable in the
electroproduction reaction $\gamma^*+A\to\rho+p+(A-1)^*$ at small $Q^2$ (where
$Q^2$ is the virtuality of the photon) but large $t$ (4-momentum transfer
squared to the knocked out proton), which represents an as-yet unexplored
kinematic region in the search for CT effects in electroproduction of vector
mesons. Calculations are also presented for the reaction $\gamma^*+D\to
J/\psi+p+n$ at JLab energies in order to determine the feasibility of measuring
the elastic $J/\psi$-nucleon scattering amplitude and/or scattering length. It
is found that it may be possible to measure the $J/\psi$-nucleon scattering
amplitude at lower energies than previous measurements, but the scattering
length cannot be measured.
