/scoreboard objectives add CobbleStorage dummy CobbleStorage

/testforblock x y z minecraft:furnace -1 {Items:[{Slot:0,id:cobblestone,Count:64}]}
--> if true (comparator or conditional chain)
/blockdata x y z {Items:[{Slot:0,id:cobblestone,Count:32}]}
-->comparator/conditional chain
/scoreboard players add <playername> CobbleStorage 32

/give @p[score_CobbleStorage_min=64,r=3] minecraft:cobblestone 64
-->Comparator/conditional chain
/scoreboard players remove @p[score_CobbleStorage_min=64,r=3] CobbleStorage 64

/setblock ~ ~ ~ minecraft:chest