The problem is the installer seems to have installed the F-104 in ALL of the sims, including the pristine, stand-alone FS9 installation on E drive as well.
That's not a "problem" at all, and the installer hasn't installed into any other sim than the one you chose at installation time. This, with "installation", meaning copying all the files needed for the airplane. They have been installed only in ONE sim, unless of course you manually copy them from one sim to another, but the installer won't install in more than one sim.
About your ACTIVATION, instead, that's not a "file" that is anywhere on your system. It's stored in the Windows REGISTRY, under your user account.
This obviously make sense because, it allows you to uninstall/reinstall both the product AND the sim as many times as you want, without worrying about your activation.
This also means that, once you activated the Serial for a product, the question shouldn't appear anymore, unless you upgrade your hardware or reinstall Windows OR switch to another user account. If you run each sim in different users accounts, you will have to confirm your activations for each of them, but this will happen only once.
After this happens, I get another series of messages, all saying the same thing and relating to the scenery packages that FSDT also offers:
"The product Cloud9 XXXXXX (Amsterdam/Aviano/Fly the Lakes/Pisa/etc) is correctly installed but not yet active on this PC. Do you want to activate it now? Yes/No." I have not purchased any of these sceneries, nor installed them on any of the sims - yet this message continues to pop up on all the sims during intro.
This is an ENTIRELY different issue and, instead, it shows you HAVE some kind of Serial key in the registry for those products. Now the question would be, why you have a Serial key for those products, when you never bought them ? If you bought the products, your Serial will work and you surely would want to activate it, but if you haven't, you have an invalid/fake serial for those products, and (I'm sorry to say this, but it's the only possible explanation), is that you tried to use an old crack for Cloud9 products that obviously doesn't work anymore now, but it left fake serials in your registry.
None of our installers or products obviously put wrong/fake serials in the registry and, even if you try to manually type a serial and make a mistake while typiing it, it won't be added to the registry by our software, unless it PASSES the activation. That's why the only possible explanation is that an external program has filled the registry with invalid data.
The only way to clean your registry, so you won't have activation requests for product you don't own, is to use the REGEDIT utility that comes with Windows, go to the following folder:
HKEY_CURRENT_USER\Software\Cloud9
and remove all the folders named as products you don't own. If you run with multiple user accounts, you must repeat this procedure by logging with each one of them.