How do I find full path to an application in a batch script

You can locate an executable on the path (or other path-like string if necessary):

c:\> for %i in (cmd.exe) do @echo. %~$PATH:i
C:\WINDOWS\system32\cmd.exe

c:\> for %i in (python.exe) do @echo. %~$PATH:i
C:\Python25\python.exe

Details can be found at the end of the help text for the "for" command, "for /?" but the summary is:

%~i    - expands %i removing any surrounding quotes.
%~fi   - expands %i to a fully qualified path name.
%~di   - expands %i to a drive letter only.
%~pi   - expands %i to a path only.
%~ni   - expands %i to a file name only.
%~xi   - expands %i to a file extension only.
%~si   - expanded path contains short names only.
%~ai   - expands %i to file attributes of file.
%~ti   - expands %i to date/time of file.
%~zi   - expands %i to size of file.
%~$P:i - searches the directories listed in the P environment variable
         and expands %i to the fully qualified name of the first one found.
         If the environment variable name is not defined or the file is not
         found by the search, then this modifier expands to the empty string.

The modifiers can be combined to get compound results:

%~dpi    - expands %i to a drive letter and path only.
%~nxi    - expands %i to a file name and extension only.
%~fsi    - expands %i to a full path name with short names only.
%~dp$P:i - searches the directories listed in the P environment variable
           for %i and expands to the drive letter and path of the first
           one found.
%~ftzai  - expands %i to a DIR like output line.

If your executable isn't on the path (as per your edit), your best bet is to use the bare/subdirectory format of dir which will do it for you. From the root directory:

dir /b /s ISTool.exe

will get you all of the files on that drive with that name. You then just have to parse the output.