Jets in blazars are an excellent forum for studying acceleration at relativistic shocks using the highly-variable emission seen across the electromagnetic spectrum. Our recent work on combining multi-wavelength leptonic emission models with complete simulated distributions from shock acceleration theory has resulted in new insights into plasma conditions in blazars. This has demonstrated the ability to infer the cyclotron frequency, the plasma density and thus also the Alfven speed, thereby determining the rapidity of particle energization. An important inference was that MHD turbulence levels decline with remoteness from jet shocks. This paper outlines new results from our recent extension of this program to a two-zone, time-evolving construction, modeling together both extended, enhanced emission states from larger radiative regions, and prompt flare events from compact acceleration zones. These are applied to flares in the FSRQ blazar 3C 279 monitored by Fermi-LAT in gamma-rays in late 2013. With impulsive injection episodes from the shock zone, as the acceleration first proceeds and then abates, the radiative simulations obtain a pronounced spectral hardening in the optical and gamma-ray bands as the flare grows, followed by a softening during the decay phase. For 3C 279, while model radio and X-ray synchrotron flares are temporally correlated, there is a lag in both bands relative to GeV gamma rays and optical emission on timescales of a number of hours. This delay is governed by the short cooling time associated with the bright external Compton signal.