Ultimately, Applemasterexpert it correct. You should contact Wikia directly about these issues. However, I will provide some speculation below.
Unfortunately, since you migrated from a private wiki, chances are some changes had to be made to adhere to Wikia's standard configuration.
The likely reason for the "stripping" of users is that Wikia uses a central account system. If some users had an account with the private wiki but don't have one with Wikia, then those accounts were probably dropped. Frankly, I am surprised any users were kept. To do that would require either 1) users' accounts with the private wiki be confirmed to belong to a particular existing Wikia user (and for Wikia to "link" those accounts) or 2) for Wikia to auto-create accounts for every user on the private wiki. My guess is they went with the latter but omitted users that were inactive on the private wiki; that way those usernames would remain open for future Wikia users.
I am not sure why they would remove the blocks. Perhaps the module version used by the private wiki was not compatible with Wikia's?
Regarding autoconfirmed users and MultipleUpload, perhaps this is also a version computability issue? Wikia certainly still has that group (or at least a similar one) (see here) and that extension.