About the drop shadows... two things might help.
1. When creating the shadow in InDesign, make sure the 'Shadow Honors other Effects' box is checked.
2. (In the Fiery's Command Work Station) If working with a CMYK file, try changing the setting 'pure black' to 'normal black' in the Properties/Color/Expert Settings/Gray and Black Processing tab. This flattens the image and is useful for some, but not all jobs with this problem.
Regarding the VDP, Especially with those large jobs and a limit on your memory, try outputting the VDP file in chunks (limit each pdf output file to a minimum size) creating a series of several files. Sometimes the smaller files ease the load on the Fiery or the printer's buffer. Just treat each file in the series as another print job. Yes, It's a workaround, but sometimes the job just needs to get done, and discussions about the finer technicalities can be done after the job is out the door.