You can usually turn to system events in these cases. System events knows about the windows of running processes and you can usually manipulate those windows. Something like this will show you some of the things you can do. Just play around with the code and see if you can do what you want.
tell application "System Events"
tell process "Whatever"
properties of windows
end tell
end tell
EDIT: One of the properties of a window is its "title". So you might be able to use that. This approach uses the fact that many applications have a "Window" menu and under that menu many times the name of the windows are listed and you can switch windows by clicking the approprite menu item. So something like this might work... my example uses TextEdit.
tell application "TextEdit" to activate
tell application "System Events"
tell process "TextEdit"
set windowTitle to title of window 2
click menu item windowTitle of menu 1 of menu bar item "Window" of menu bar 1
end tell
end tell