Code:
<Hotkey Alt Ctrl L>
<LaunchAndRename Local "D:\Games\World of Warcraft\Wow.exe" WoW1 1>
<LaunchAndRename Local "D:\Games\World of Warcraft\Wow.exe" WoW2 2>
<Command ResizeAndPosition WoW1 WoW2>

<Hotkey Ctrl R>
   <SendPC Local>
      <Command Rename local "World of Warcraft" "WoW1">
      <Command Rename local "World of Warcraft" "WoW2">

<Hotkey F1>
   <Command ResizeAndPosition WoW1 WoW2>
<Hotkey F2>
   <Command ResizeAndPosition WoW2 WoW1>
You can't establish a command in a hotkey. The Command needs to be established in a subroutine before it is used.

Which means the ResizeAndPosition Subroutine needs to be established before it is called - move it under the LaunchAndRename Subroutine

Code:
//-----------------------------------------------------------
// SUBROUTINE TO LAUNCH AND RENAME A COPY OF WOW.
//-----------------------------------------------------------
<Command LaunchAndRename>
   <SendPC %1%>
  <Run %2%>
  <RenameTargetWin %3%>
  <RemoveWinFrame>
  <SetAffinity %4%>
  
//-----------------------------------------------------------
// SUBROUTINE TO Position Windows for 5 boxing.
//-----------------------------------------------------------
<Command ResizeAndPosition>
   <SendPC Local>
      <SendWinM %1%>
               <SetWinRect 0 0 1920 1080>              
      <SendWinM %2%>
             <SetWinRect 1920 0 1920 1080>
You don't have a subroutine that establishes what "Rename" does

Code:
<Hotkey Ctrl R>
   <SendPC Local>
      <Rename local "World of Warcraft" "WoW1">
      <Rename local "World of Warcraft" "WoW2">
You either need to establish a subroutine for it or remove it.

Hotkey "c Shift ..." is not a valid key.

Code:
<Hotkey c Shift LButton, MButton, RButton>  
<SendLabel w1, w2>
<KeyDown shift c>
<ClickMouse  %TriggerMainKey%>
<KeyUp shift>
Modifiers need to be listed first in the hotkey. If the c's here are a typo, you need to remove them. If not, you either need to call C a key stating that you want Shift + C to be a broadcasted key - which it already is according to the Keylist and thus redundant here :

Line 85 in C:\Users\Giga-Mu-Fin\Desktop\new 2.txt: <Hotkey Shift c, LButton, MButton, RButton>
00:53:49: <Hotkey Shift C> has already been defined. Only the first definition will be used.
or define C as a modifier, which means it must added to the Keylist as an exclusion. If you actually intended on sending C, you also need to include it in the Keyup.

Code:
//================================================================
// SAMPLE SCRIPT FOR TWO WOW'S ON ONE PC
//
// Instructions: Copy this entire script (all the blue writing
// on gray background including comments). Save it in a file.
// Load it into HotkeyNet.
//
// Toggle the scroll lock key to turn hotkeys off and on. (You
// can change this if you want, just like you can change
// everything else with HotkeyNet.)
//
// Requires HotkeyNet build 147 or higher.
//
// For more info, go to www.hotkeynet.com
//================================================================

//-----------------------------------------------------------
// SUBROUTINE TO LAUNCH AND RENAME A COPY OF WOW.
//-----------------------------------------------------------
<Command LaunchAndRename>
   <SendPC %1%>
  <Run %2%>
  <RenameTargetWin %3%>
  <RemoveWinFrame>
  <SetAffinity %4%>
  
//-----------------------------------------------------------
// SUBROUTINE TO Position Windows for 5 boxing.
//-----------------------------------------------------------
<Command ResizeAndPosition>
   <SendPC Local>
      <SendWinM %1%>
               <SetWinRect 0 0 1920 1080>              
      <SendWinM %2%>
             <SetWinRect 1920 0 1920 1080>  

//-----------------------------------------------------------
// HOTKEY TO LAUNCH AND RENAME YOUR WOW WINDOWS while 5 boxing
// Please configure the Path and processor afinitys correctly
//-----------------------------------------------------------
<Hotkey Alt Ctrl L>
<LaunchAndRename Local "D:\Games\World of Warcraft\Wow.exe" WoW1 1>
<LaunchAndRename Local "D:\Games\World of Warcraft\Wow.exe" WoW2 2>
<ResizeAndPosition WoW1 WoW2>


//----------------------------------------------------------------
//Window Switching
//----------------------------------------------------------------
<Hotkey F1>
   <ResizeAndPosition WoW1 WoW2>
<Hotkey F2>
   <ResizeAndPosition WoW2 WoW1>

//-----------------------------------------------------------
// DEFINE MAIL LABELS FOR SENDING KEY STROKES.
//-----------------------------------------------------------
<Label w1 Local SendWinM WoW1>
<Label w2 Local SendWinM WoW2>


//-----------------------------------------------------------
// DEFINE HOTKEYS FOR ALL KEY COMBINATIONS THAT WILL GET
// SENT TO ALL WOWS. ADD MORE KEY COMBO'S IF YOU WANT.
//-----------------------------------------------------------
<KeyList MyList A-Z, 0-9, Enter, Tab, Oem4, Space, Comma, Oem6 except W, A, S, D, Q, E, L>

<Hotkey MyList; Shift MyList; Alt MyList; Ctrl MyList>
       <SendLabel w1, w2>
       <Key %Trigger%>
//-----------------------------------------------------------
// DEFINE MOVEMENT KEYS THAT WILL GET SENT TO BOTH WOW'S.
// ADD MORE KEYS IF YOU WANT.
//-----------------------------------------------------------
<MovementHotkey ScrollLockOn up, down, left, right>
<SendLabel w1, w2>
<Key %Trigger%>

<Hotkey Shift LButton, MButton, RButton>  
<SendLabel w1, w2>
<KeyDown shift>
<ClickMouse  %TriggerMainKey%>
<KeyUp shift>

<hotkey pause>
    <sendpc local>
    <ToggleHotkeys>