To answer your points:

• KiXtart script with no suffix.
  The "'Script error : failed to find/open script !" error is a feature (bug?) of KiXtart.
  You will find that "kix32.exe code" will also produce this error, and that "kix32.exe code." will work.
  
• -d produces output in crypted.exe
  This is by design. The idea is that you can create a debug version for testing. When you are ready to release to your users you don't use the "-d" flag. NB For security reasons you cannot used the "-d" flag with "crypted.exe" - it has to be set on when you run kixcrypt.exe.
  
• -p password causes divide zero error
  Fixed in version 2.04a
  
• Temporary file names.
  As of version 2.04a the numbered file name is not used, so cannot easily be guessed. A file name of 8 random upper case letters is used. 1000 of these are tried before the program gives up. Each time crypted.exe is tun the random file names will be different.
  
• kc000000 directory.
  As of version 2.04a a directory with the same name as the temporary file will not cause crypted.exe to exit.

The crypted.exe has to create a temporary file because KiXtart cannot accept piped input. The current directory is always used and I probably won't be changing that simply because it would mean a lot of work for very little benefit.
If the directory is not writable by the user you will get the "Cannot open temp file for writing" error.

If you need to redirect the temporary file to another direcectory then "CD" to it before running crypted.exe

You (and anyone else) are more than welcome to publish the KixCrypt utility on your site.

I hope that answers all your questions.