Hmm, I think I figured it out: [EDIT: Found a problem with it, this is corrected version]

[code:1]WinGet, wowid, List, World of Warcraft


WinMinimize, ahk_id %wowid1%
WinMinimize, ahk_id %wowid2%
WinMinimize, ahk_id %wowid3%
WinMinimize, ahk_id %wowid4%
WinMinimize, ahk_id %wowid5%



WinActivate, ahk_id %wowid1%

MsgBox, 4,, Is this your WOW Main window? (press Yes or No)

IfMsgBox Yes
{
idMain = %wowid1%
idA = %wowid2%
idB = %wowid3%
idC = %wowid4%
idD = %wowid5%

}
else IfMsgBox No
{

WinMinimize, ahk_id %wowid1%
WinMinimize, ahk_id %wowid2%
WinMinimize, ahk_id %wowid3%
WinMinimize, ahk_id %wowid4%
WinMinimize, ahk_id %wowid5%

WinActivate, ahk_id %wowid2%
MsgBox, 4,, Is this your WOW Main window? (press Yes or No)

IfMsgBox Yes
{
idMain = %wowid2%
idA = %wowid1%
idB = %wowid3%
idC = %wowid4%
idD = %wowid5%
}
else IfMsgBox No
{

WinMinimize, ahk_id %wowid1%
WinMinimize, ahk_id %wowid2%
WinMinimize, ahk_id %wowid3%
WinMinimize, ahk_id %wowid4%
WinMinimize, ahk_id %wowid5%

WinActivate, ahk_id %wowid3%
MsgBox, 4,, Is this your WOW Main window? (press Yes or No)

IfMsgBox Yes
{
idMain = %wowid3%
idA = %wowid1%
idB = %wowid2%
idC = %wowid4%
idD = %wowid5%
}
else IfMsgBox No
{
WinMinimize, ahk_id %wowid1%
WinMinimize, ahk_id %wowid2%
WinMinimize, ahk_id %wowid3%
WinMinimize, ahk_id %wowid4%
WinMinimize, ahk_id %wowid5%

WinActivate, ahk_id %wowid4%
MsgBox, 4,, Is this your WOW Main window? (press Yes or No)

IfMsgBox Yes
{
idMain = %wowid4%
idA = %wowid1%
idB = %wowid2%
idC = %wowid3%
idD = %wowid5%
}
else IfMsgBox No
{
WinMinimize, ahk_id %wowid1%
WinMinimize, ahk_id %wowid2%
WinMinimize, ahk_id %wowid3%
WinMinimize, ahk_id %wowid4%
WinMinimize, ahk_id %wowid5%

WinActivate, ahk_id %wowid5%
MsgBox, 4,, Is this your WOW Main window? (press Yes or No)

IfMsgBox Yes
{
idMain = %wowid5%
idA = %wowid1%
idB = %wowid2%
idC = %wowid3%
idD = %wowid4%
}
else IfMsgBox No
{
MsgBox There was an issue determining the main window, please reload script or load another.

}
}
}
}
}
[/code:1]