giving an Item Entity a specific scoreboard number was the only way of locating and manipulating the item entity, now it doesnt work anymore in 1.8.8
wich is a big downfall for any custom map that requires /entitydata at a specific item..
my command block system didnt work and i folowed the problem down to its core.
the commands used:

This one makes shure that a specific item gets a scoreboard DropSwap of 16, as direct Execute at & testfor & entitydata doesnt work on item entities that include NBT:

/scoreboard players set @e[type=Item] DropSwap 16 {Item:{Damage:0s,id:"minecraft:porkchop"}}

this one makes shure that all items that have a scoreboard of 16 turn into a different item entity, as soon as my HeatBlade Scoreboard is 1:

execute @a[score_HeatBlade_min=1] ~ ~ ~ entitydata @e[r=5,score_DropSwap_min=16,score_DropSwap=16] {Item:{Damage:0s,id:"minecraft:cooked_porkchop",tag:{display:{Name:"cooked_porkchop"}}}}

this command resets the HeatBlade scoreboard back to 0:

execute @a[score_HeatBlade_min=1] ~ ~ ~ execute @e[type=Item,score_DropSwap_min=16,score_DropSwap=16] ~ ~ ~ scoreboard players set @a HeatBlade 0

What i expected:
the raw porkchop turns into a cooked version as soon as i swing my blade at the pigs and kill them.

What happened instead:
the items did not change at all

Steps to reproduce:
create a scoreboard that is called HeatBlade as Stat.UseItem.minecraft:Iron_Sword
then crate the famous superfast command block clock by sethbling.
make shure you put all 3 of the commands above into a command block and place them right next to the redstone blocks of the superfast clock, so that all 3 get powered 20 times in a second. swing at a pig with an iron sword to kill them and wait untill the raw meat turns cooked.

My Conclusion:
it worked before 1.8.7, i suppose that the third command doesnt care about how much scoreboard the item entity has so that he skips it and turns My HeatBlade scoreboard back to 0 a bit too fast. i found that out by changing the scoreboard output to something different than 16, but it still choose to change the pork to a cooked version, also further testing revealed that only the meat of the first pigs get changed, all the other raw pork stays how it is.
meaning that the items dont have enough time to turn, because the 3rd command does only care if there is any item on the floor.