I am very familiar with Encore. It should be as simple as unmuting the necessary outputs and adjusting the proper playback options in the Staff Sheet window and then going to File->Save As, where you'll have the option of selecting MIDI (Type 1) as a filetype.
Yup, Passport was bought out by GVOX. They revamped the code for Windows XP about five or six years ago and started distributing it, along with MusicTime Deluxe and Master Tracks Pro. They're all a bit dated, but I just checked the website and it has received a heavy upgrade since I last looked, suggesting there is some development going on.
Current version of Encore is 4.5.5. The Beta of 4.6 is in testing, according to the site, and the PR seems to make it a very big improvement.