I store my motorcycle over winter every year and have gad my GTO in storage for longer than I like to think about. I had a friend that recently got deployed overseas for a an undetermined amount of time that asked me what he should do to store his truck. Keep in mind that I've never stored a diesel for any significant time so this is based off of gasser experience. Here's what I sent him:
What I would do is right before you put it into storage change the oil and filter and then take it on a 20-30 mile drive. You want it to be long enough to warm up the engine completely - that will burn any moisture out of the oil. You don't want to store it with old oil in there because the acids in the used oil will just sit there and eat away at stuff. Then park it (inside of course) and put it up on jack stands at all four corners (with the stands on the axles themselves, not the frame). Put some desicant packs in the interior to keep moisture and smells out of the interior and leave the windows slightly cracked for air flow. Then remove the batteries and put them in a heated house somewhere - preferrably with someone that you know that could put them on a charger every month or so. Put some mothballs in a few places in the engine bay (that will keep rodents out of the engine and electronics). That's basically how I store my motorcycle over winter with the exception that I also put fogging oil into the cylinders - but I can't think of any way of doing that with a diesel or if it would even be advisable. Oh yeah, I'd go ahead and wash it and clean the windows inside and out right before putting it away too - that way nothing other than dust is sitting on the paint for all that time.