<<What is the best procedure for storing a diesel? Just change the oil before putting it away.
<<Will the tires develop flat spots if I leave it parked 3 months in the garage this winter?>> Probably. Ten miles of driving will normalize them. <<Should I take the battery into the warm house or leave it in the cold garage with a trickle charger.> Not a trickle charger unless you want to kill the battery. Use a battery maintainer. Rhode Island ain't the Yukon, after all. RLE/Seattle