Minecraft – How to use /setblock and what are the possible options

When checking pre-existing NBT data, such as for /testfor, /scoreboard, or /testforblock, you must specify all data exactly as it's stored. This includes datatypes; you've declared Damage as an Integer, when instead it's saved as a Short. To declare it as a Short, you must append the value with an s:

/testfor @e[type=Item] {Item:{id:"minecraft:stained_glass_pane",Damage:4s}}

/setblock does not support replacing specific blocks. The /fill command does:

/fill x1 y1 z1 x2 y2 z2 block1 0 replace block2 0

However, if "block1" is a tile entity, then you cannot replace a specific block and must instead supply NBT data. See this explanation by Searge:

Replacing blocks with tile entities is not supported, this is due to a limitation in the parsing of commands. It may be changed in the future, but not until after 1.8.

A chest is a tile entity, meaning you cannot use this to replace a specific block with a chest.

As a work-around, you could detect the existence of the particular block first using /testforblock:

/testforblock x y z minecraft:stone 0

And then use /setblock if that command succeeded:

/setblock x y z minecraft:chest