Hmm I'm afraid I don't understand this matter about "intalling the original into krprotect setup" :(That works, I believe. I assume once you install the original into krprotect setup, it is rewritten somewhere else for safekeeping. Just remember when Klaus updates the version, be sure to use the krpano.swf from the download package for the kprotect setup, (only done once at each version changeover) and you should be fine. In other words, don't use a tour that is named krpano.swf in the SETUP of kprotect. I hope I am clear on this.
I always output as krpano.swf and yes on keeping just the first html.