Hello Alan,
Thank you for purchasing a license!
and having some trouble with the file transfer portion of the app
Sorry for that, we will be re-writing the File Transfer module some time soon.
While setting up the MSI Installer, I had an idea about the email notification portion that I wanted to share. Paid users could have an online account that links to their installer that allows them to configure some of the extra options such as the authentication and email notifications of a new ID being generated. Then the application rather than sending the notifications through SMTP could relay that info to RemoteUtilities (or other repeater?) where the info could then be emailed to the user.
Implementing an online account is indeed in our plans for the future. However, making the installer send emails via our company-hosted script would be a step back to the mechanism which we have abandoned in favor of the "SMTP method".
The difference is that if the host gets decompiled, there is a chance of disclosure of where the emails are being sent, and maybe passwords as well. As it is I created a new gmail account, set it to forward to my normal account and then deletes it, wrote a script that auto flushes the trash every minute on that account so there is no record of it.
If you mean Host access passwords, they are not disclosed. When you choose "Automatically generate Host password" the password is encrypted with a public key on the Host side. In order to decrypt it one needs the private key which only resides on the Viewer side, initially in the Viewer where you actually built the installer although you can also copy the key to another Viewer.
If you mean the SMTP password though, it's indeed can be extracted from the installer but that's "by design". There is simply no other way to simultaneously protect the SMTP password and use it on the same Host. We explicitly warn the user about this:

Also, we do suggest that the user avoid entering their primary email account credentials and instead use a "disposable" email account for that single purpose of receiving Host notifications. Even if someone gets access to those emails they won't be able to connect to Hosts because of the above mentioned reasons - they won't be able to find out the password because it is never sent plain in an email. Besides, there is also two-factor authentication which can be enabled for added security.
Let us know if you have any questions. Thanks.