The VM one contained full updates for the adsp, emmcboot, recovery, boot, and osbl. The stuff in /system were distributed as patch files if they were files that already existed. It is already a flashable zip when it is downloaded onto your phone. You can pull it right off the phone before it gets installed and deleted.
Being that the zip was mostly patch files, it wouldn't restore any files that were deleted, and probably wont restore files that were altered (like if you applied a custom theme into your system apks). It will, however, bork the su binary by removing the suid bit. It will overwrite any custom kernel you have installed, and it will probably remove any custom recovery the first time it boots up.
Your best bet is to let the update install over an un-rommed & unthemed stock rom, reroot your phone, and then manually extract all the files after they are patched by the update so you can build a zip yourself. Aside from that, you can extract all the files and patch them on your computer, or you can wait until somebody buys a new sprint phone that comes from the store with the update.
