You can wrap code in a timeout block. The timeout of commands (events) can be changed if the default time of 60 seconds is too short (or long). Just replace the comments below with the open command.
with timeout of 3000 seconds
-- insert commands here that takes longer than 60 seconds to complete
end timeout
Or replace the handler you’re using to open documents:
on openFile(thePath)
with timeout of 3000 seconds
tell application "QuarkXPress" to open alias thePath with Suppress All Warnings
end timeout
end openFile