1. All bode plot (AC) simulations are based upon linear models in the frequency domain, both in MATLAB and Spice simulators. A transistor level simulation in Spice is done in the time domain, so you would have to generate a plot from data generated from single frequency simulations at different frequencies of interest.
2. Not that familiar with Spectre but I suspect it makes little difference.
3. Transient simulations of circuits that have high frequency carrier with a low frequency feedback loop (such as a PLL or Switching Power Supplies) take a long time to settle because of the many thousand of cycles of the carrier needed for the loop to stabilize and reach a steady output. Generally the only way to speed that up is a faster computer or a simulation program designed to efficiently run on a multi-processor computer. Reducing the simulation accuracy parameters may increase the speed some but at the expense of accuracy.