Welcome, Steve.
As a general point, you'll have to appreciate the program is designed as a
movie database, not a movie
media database. So this means there's no special accommodation for managing multiple forms of media per movie, or DVD-related features like bar code scanning and the downloading of information about specific media (like DVD features). Such features may be added in time, but they're not a high priority. That being said, PVD is a very flexible and powerful database, so it can be adapted to most situations and preferences.
If using ID for your disc number concerns you (because it can be re-indexed), the alternative is to use a custom field.
As for multiple forms of media, you'll have to decide what works best for you. One approach is to maintain a separate record for each.
This topic discusses ways to manage such "duplicate" records. The alternative is to maintain just one record per movie, scan just one type (or the "best" available) media, and record information about additional media in custom fields.
If you're just starting, the most important consideration (especially if you have 5000 disks) should probably be importing information from
Movie Collector. I don't recommend worrying about downloaded information. Even if you're attached to it, you're not going to be able to maintain the data provided by
Movie Collector. The information you should try to transfer is anything "personal," like view dates, ratings, comments, media location and disk numbers. From
this post, it's evident importing data from
Movie Collector via Excel is feasible. While this one doesn't go into how, many other topics do (you should be able to find them using the forum
Search facility).