Part 2:

Code:
 //-----------------------------------------------------------// Template: Conditional1
//
// %1% - Alt Ctrl Shift %1% identifier for the conditions
// %2% - Window name at position 5 in first condition
// %3% - Window position number of window to swap with %2%
// %4% - Window name at position %3%
// %5% - Window name at position 5 in second condition
//-----------------------------------------------------------
<Template Conditional1>
    <Hotkey Alt Ctrl Shift %1%>
        <If Win5 Is WoW%2%>
            <Swap%3%And5 WoW%4% WoW%2%>
        <Else If Win5 Is WoW%5%>
            <Swap%3%And5 WoW%4% WoW%5%>
        <EndIf>
<EndTemplate>


//-----------------------------------------------------------
// Template: Conditional2
//
// %1% - Alt Ctrl Shift %1% identifier for the conditions
// %2% - Window name at position 5 in first condition
// %3% - Window position number of window to swap with %2%
// %4% - Window name at position %3%
// %5% - Window name at position 5 in second condition
// %6% - Hotkey to call if the other two conditions fail
//-----------------------------------------------------------
<Template Conditional2>
    <Hotkey Alt Ctrl Shift %1%>
        <If Win5 Is WoW%2%>
            <Swap%3%And5 WoW%4% WoW%2%>
        <Else If Win5 Is WoW%5%>
            <Swap%3%And5 WoW%4% WoW%5%>
        <Else>
            <DoHotkey Hotkey Alt Ctrl Shift %6%>
        <EndIf>
<EndTemplate>


//-----------------------------------------------------------
// Template: Conditional3
//
// %1% - Alt Ctrl Shift %1% identifier for the conditions
// %2% - Window name at position 3 or 4 in the conditional
// %3% - Hotkey to call if first condition succeeds 
// %4% - Hotkey to call if second condition succeeds
//-----------------------------------------------------------
<Template Conditional3>
    <Hotkey Alt Ctrl Shift %1%>
        <If Win3 Is WoW%2%>
            <DoHotkey Hotkey Alt Ctrl Shift %3%>
        <Else If Win4 Is WoW%2%>
            <DoHotkey Hotkey Alt Ctrl Shift %4%>    
        <EndIf>
<EndTemplate>


//-----------------------------------------------------------
// Template: Conditional4
//
// %1% - Alt Ctrl Shift %1% identifier for the conditions
// %2% - Window position to check in the condition statement
// %3% - Window name at position %2% in the condition statement
// %4% - Hotkey to call if the condition succeeds 
// %5% - Hotkey to call if the condition fails
//-----------------------------------------------------------
<Template Conditional4>
    <Hotkey Alt Ctrl Shift %1%>
        <If Win%2% Is WoW%3%>
            <DoHotkey Hotkey Alt Ctrl Shift %4%>
        <Else>
            <DoHotkey Hotkey Alt Ctrl Shift %5%>
        <EndIf>
<EndTemplate>


//----------------------------------------------- Win4 - WoW1
// Alt Ctrl X
// If MouseIsOverWindow WoW1
// If Win4 Is WoW1 (caller: Alt Ctrl Shift .)
//
// ----------------------------------------- Alt Ctrl Shift /
//
//-----------------------------------------------------------
<ApplyTemplate Conditional1 Oem2 4 4 1 5>


//----------------------------------------------- Win4 - WoW1
// Alt Ctrl X
// If MouseIsOverWindow WoW1
// If Win4 Is WoW1 (caller: Alt Ctrl Shift N)
//
// ----------------------------------------- Alt Ctrl Shift .
//
//-----------------------------------------------------------
<ApplyTemplate Conditional2 Period 2 4 1 3 Oem2>


//----------------------------------------------- Win3 - WoW1
// Alt Ctrl X
// If MouseIsOverWindow WoW1
// If Win3 Is WoW1 (caller: Alt Ctrl Shift M)
//
// ----------------------------------------- Alt Ctrl Shift ,
//
//-----------------------------------------------------------
<ApplyTemplate Conditional1 Comma 4 3 1 5>


//----------------------------------------------- Win3 - WoW1
// Alt Ctrl X
// If MouseIsOverWindow WoW1
// If Win3 Is WoW1 (Alt Ctrl Shift N)
//
// ----------------------------------------- Alt Ctrl Shift M
//
//-----------------------------------------------------------
<ApplyTemplate Conditional2 M 2 3 1 3 Comma>


//------------------------------------------------------ WoW1
// Alt Ctrl X
// If MouseIsOverWindow WoW1 (caller: Alt Ctrl Shift C)
//
// ----------------------------------------- Alt Ctrl Shift N
//
//-----------------------------------------------------------
<ApplyTemplate Conditional3 N 1 M Period>


//----------------------------------------------- Win2 - WoW1
// Alt Ctrl X
// If MouseIsOverWindow WoW1
// If Win2 Is WoW1 (caller: Alt Ctrl Shift V)
//
// ----------------------------------------- Alt Ctrl Shift B
//
//-----------------------------------------------------------
<ApplyTemplate Conditional1 B 4 2 1 5>


//----------------------------------------------- Win2 - WoW1
// Alt Ctrl X
// If MouseIsOverWindow WoW1
// If Win2 Is WoW1 (caller: Alt Ctrl Shift C)
//
// ----------------------------------------- Alt Ctrl Shift V
//
//-----------------------------------------------------------
<ApplyTemplate Conditional2 V 2 2 1 3 B>


//------------------------------------------------------ WoW1
// Alt Ctrl X
// If MouseIsOverWindow WoW1 (caller: Alt Ctrl Shift Oem5)
//
// ----------------------------------------- Alt Ctrl Shift C
//
//-----------------------------------------------------------
<ApplyTemplate Conditional4 C 2 1 V N>


//----------------------------------------------- Win1 - WoW1
// Alt Ctrl X
// If MouseIsOverWindow WoW1
// If Win1 Is WoW1 (caller: Alt Ctrl Shift Z)
//
// ----------------------------------------- Alt Ctrl Shift X
//
//-----------------------------------------------------------
<ApplyTemplate Conditional1 X 4 1 1 5>


//----------------------------------------------- Win1 - WoW1
// Alt Ctrl X
// If MouseIsOverWindow WoW1
// If Win1 Is WoW1 (caller: Alt Ctrl Shift Oem5)
//
// ----------------------------------------- Alt Ctrl Shift Z
//
//-----------------------------------------------------------
<ApplyTemplate Conditional2 Z 2 1 1 3 X>


//------------------------------------------------------ WoW1
// Set WoW1 Main Window
//------------------------------------------------------ WoW1
// Alt Ctrl X
// If MouseIsOverWindow WoW1 (caller: Alt Ctrl F6)
//
// ----------------------------------------- Alt Ctrl Shift \
//
//-----------------------------------------------------------
<ApplyTemplate Conditional4 "Oem5; Alt Ctrl F1" 1 1 Z C>


//----------------------------------------------- Win4 - WoW2
// Alt Ctrl X
// If MouseIsOverWindow WoW2
// If Win4 Is WoW2 (caller: Alt Ctrl Shift ;)
//
// ----------------------------------------- Alt Ctrl Shift '
//
//-----------------------------------------------------------
<ApplyTemplate Conditional1 Oem3 4 4 2 5>


//----------------------------------------------- Win4 - WoW2
// Alt Ctrl X
// If MouseIsOverWindow WoW2
// If Win4 Is WoW2 (caller: Alt Ctrl Shift J)
//
// ----------------------------------------- Alt Ctrl Shift ;
//
//-----------------------------------------------------------
<ApplyTemplate Conditional2 Oem1 1 4 2 3 Oem3>


//----------------------------------------------- Win3 - WoW2
// Alt Ctrl X
// If MouseIsOverWindow WoW2
// If Win3 Is WoW2 (caller: Alt Ctrl Shift K)
//
// ----------------------------------------- Alt Ctrl Shift L
//
//-----------------------------------------------------------
<ApplyTemplate Conditional1 L 4 3 2 5>