Minecraft – /replace unspecific item

Use the replaceitem command. For example to replace the slot 23 with iron_boots the command should be:

/replaceitem block 6 11 -13 slot.container.24 iron_boots 1

Click here for more info on replaceitem.

You'll need to "translate" the glass bottle data tag into something that works with target selectors (@a and so on). This can be achieved most easily using dummy scoreboard values or, in 1.9, scoreboard tags.

In 1.8, create an objective using

scoreboard objectives add bottleInOne dummy

Create a fill clock and run the following two commands

scoreboard players set @a[score_bottleInOne_min=1] bottleInOne 0
scoreboard players set @a[score_bottleInOne=0] bottleInOne 1 {SelectedItemSlot:0,SelectedItem:{id:minecraft:glass_bottle}}

If the team part is necessary, you can now add @a[score_bottleInOne_min=1] to the team, and remove @a[score_bottleInOne=0] from it, using the same fill clock. You could also use these target selectors directly for the /effect and /replaceitem commands, if the team part was just your idea of selecting that player for the effect.

In 1.9, you can omit the scoreboard objective in favor of tags. Using a Repeat/Chain command block chain, run

scoreboard players tag @a[tag=bottleInOne] remove bottleInOne
scoreboard players tag @a[tag=!bottleInOne] add bottleInOne {SelectedItemSlot:0,SelectedItem:{id:minecraft:glass_bottle}}

In the following commands, you can then use @a[tag=bottleInOne] or @a[tag=!bottleInOne] to target players with and without the bottle selected in slot 0, respectively.