Thanks for your questions and if you are interested in more information you should check out the blog dedicated to CataBlog.
Now for your questions:
1. No CataBlog does not support native pagination. Personally I don't understand why so many people want it. CataBlog does work with other pagination solutions, such as multiple posts/pages, tab plugins, or built in separators such as
<!--nextpage-->. Simply make a few categories in your catalog and when adding the ShortCodes use the category filter.
2. Yes you may upload your catalog with FTP, you may also import and export your catalog database data in CSV and XML format. Read this article for more information.
Also note that CataBlog does work with MultiSite installations of WordPress. I have not tested it in 3.1 MS, but have tested it in 3.0.5 MS and 3.1 normal.