Using Automator for app to create .ISO

I have a couple of observations...

There's nothing inherently wrong with your script - it's essentially gathering all the data, then firing off a single shell command to do the work. The problem is that to extend the functionality to the point of creating an .iso, you need to do that within the shell command.

An alternative (easier - at least for an experienced AppleScripter) path would be to minimize the shell command to the bare minimum (i.e. process an individual file), and use AppleScript to handle the looping and variables. For example, instead of building one string of files and passing that to one shell command that iterates over it, I'd do something more like:

tell application "Terminal"

activate

repeat with file_ in input

set filesString to quoted form of (POSIX path of file_)

do script "/Users/Mike/Documents/Scripts/ffmpeg -i " & fileString & " -acodec pcm_s16le -vcodec v210 -level 1 -coder 1 -context 1 -g 1 -qscale 0 " & fileString & ".mov"

end repeat

end tell

Now you have each specific file in an AppleScript variable (file_), which is passed in to a shell command that executes your command. Multiple input files just invoke the shell command multiple times. This also makes it easier to add processing per file

As for the other question - selecting the output file name/location, just replace your 'choose folder' with 'choose file name'. This will allow the user to specify a file name and directory using the standard UI, from which you can extract the data you want:

repeat with file_ in input

-- this works out the input file's name:

tell application "System Events"

set inputFilename to name of (get properties of file_)

end tell

-- prompt the user for where this file should be saved

set outputFile to choose file name with prompt "Specify output file name for " & inputFilename

set inputFilePath to quoted form of (POSIX path of file_)

set outputFilePath to quoted form of (POSIX path of outputFile)

tell application "Terminal"

activate

do script "/Users/Mike/Documents/Scripts/ffmpeg -i " & inputFilePath & " -acodec pcm_s16le -vcodec v210 -level 1 -coder 1 -context 1 -g 1 -qscale 0 " & outputFilePath

end tell

end repeat

Note also that I've separated the code into more logical (to me, at least) chunks... I've separated out the application logic regarding the input and output files, and just target Terminal.app with the specific command(s) that are relevant to it.

From here you can easily incorporate additional 'do script' commands to do whatever you want, using the same variables to map the input and output file names.