Just uploaded a new version of TextOverlayTool that might solve your problem.  Again, it depends on whether your application is Full Screen, or Full Screen Windowed.  If it's full screen, it would require a lot of low level coding and display via the mechanism it is using to draw, i.e. OpenGL or DirectX.  If it's fullscreen windowed, this should work.

I mentioned above I cannot use Full Screen.  I can only use windowed mode, so you're safe there.  I'll give it a test and report back.  Thanks.

Hmmm.. that's the class in C#.  I haven't worked in AHK much... what is it actually looking for?  The name?  Or the Handle?

I found this.. .maybe it could be wrapped up to get the window class that AHK is looking for?

WinGetClass, class, A
MsgBox, The active window's class is "%class%".

http://ahkscript.org/docs/commands/WinGetClass.htm

It looks like it's the active window for that one declaration.  You can use the window title or text to get it also.

I'll try also when I get home.  Never worked with AHK, and this looks like a good excuse to try

Using AHK, This is what I was able to get:

---------------------------
GetWindowClass.ahk
---------------------------
The active window's class is "HwndWrapper[TextOverlayTool.exe;;ad8ebf4a-4653-4ee9-ad96-c472c3c202f6]".
---------------------------
OK 
---------------------------

And that was with that default code.  You just have to click on the TextOverlayTool window and click the hotkey.  And I get what you mean by windowspy now- the utility that comes with AHK.

With that, I figured out the problem.  There is a guid attached to the window - I guess to disambiguate multiple instances.  Notice the guid at the end of mine is different than the guid at the end of yours.  You'll have to use the following in your code:

#SingleInstance ignore
#NoEnv
SendMode Input
SetWorkingDir %A_ScriptDir%
return

; instead of Progman for desktop change to the
; class for Flight Simulator (use WinSpy to get it)
SetTitleMatchMode, Regex
#IfWinActive ahk_class FS98MAIN
$Down::
; instead of class for Notepad use the class
; for Stickies
ControlSend,,{Down},ahk_class HwndWrapper\[TextOverlayTool.exe;;[\da-f\-]+]
return

What follows is the script that I actually used:

^k::
	SetTitleMatchMode, Regex
	totclass = HwndWrapper\[TextOverlayTool.exe;;[\da-f\-]+]
	WinGetClass, class, A
	IfWinExist, ahk_class %totclass%
	{
		WinActivate  ; Automatically uses the window found above.
		Send, {Up}
	}
	WinActivate ahk_class %class%
	
return

It's a bit messy, and won't work for markdown files as the control can't get a focus in that case, so I'd have to manually focus it.  But for your purposes, as long as you load the file and set the cursor into the control, it should work.

And it was an interesting delve into AHK.  I used the basic version, as I wasn't sure that the other version would work with SciTE4AutoHotkey, and I wanted debugging to see what was going on.  But it was easy to get up and running in it.

Playing around some more- there's another problem that if something else is modal (SSC screen for instance), then I can't make it on top while it's modal, then after, it doesn't become topmost again, because I already tried and failed.  *sigh*

@MilesAhead - Thanks for that heads-up.  It looks like a good resource, but I probably need to learn AHK better so I can ask intelligent questions.

They have no problem helping newbs to the language.  About the only things that annoy the regulars there are things like saying "it doesn't work" without telling what happens when it doesn't work or "I get errors" without specifying the errors, or refusal to post a test case that shows the problem.

Everyone has a bit of trouble with AHK syntax when starting out since it mixes old and new syntax styles.

But in any case it's up to you.