I dont know if you succeeded in this problem, but I would be very interested to have fresh news.

As a side note, I had problems compiling your C program, until I added

#include <stdio.h>
#include <X11/Xlib.h>
#include <X11/Xutil.h>
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moreover, I was unable to run the perl program: I let it collect the xid by:

$window_id_of_program_to_embed=`getwindowid2 $windowname`;
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(where getwindowid2 is your C program, which outputs just the numerical idof any window named $windowname)

the program just creates an empty box, without errors/warnings, and the app to be embedded just stays there.

Any idea?

alessandro