aicranham's caution that the first consideration is to break up a 3.5 cm stone with lithotripsy is right on the mark.  For a stone that size, surgery would be a reasonable alternative.  Other approaches should be regarded as prophylactic, to make sure this doesn't happen again.

Regarding diet, the Life Extension Foundation (www.lef.org) reported a study showing that some soybean products have oxalate levels that may be too high for someone with a history of kidney stones.  Their citation is:  J Agric Food Chem. 2001 Sep;49(9):4262-6.

Adequate hydration--drinking a lot of water--is an important consideration.