I'll take a stab ... see yin and yang.
#1: since you started a long time ago, the mdl_user data table actually might contain salted passwords and your config.php file has a password salt line (maybe more than one)? If that's the case, wouldn't attempt import of table from old site into new. Could, however, import all new via csv. Use LDAP? Then no need to re-create users. See #2
#2: if the backups are full backups including users, users in the course should restore. But be aware of role conflicts/overrides. And you'll be restoring assignments and their files - stuff that should be removed. Should re-set the 2.2 courses before restoring those backups to avoid the assignments issue, but then you also loose users enrolled.
#3: I'd say no. Course ID's are still assigned upwards ... ie, you delete a course, Moodle doesn't re-use that course ID number, but, rather, assigns the next highest available course ID.
'integrated with other' means what? Just links? Well, then yes, those links will be broken in that they will not point to the same course ID.
To facilitate restoring those 2.2.x courses (assuming you might have many), suggest leaving the 2.2 site up and running. Review the setup for autobackups ... might turn off saving users in the autobackups. Turn on autobackups and point it to a file system repo for m22backups. The m22backups directory is accessible to the 2.6 - mount point/nfs share or whatever. Pick a weekend and begin the autobackups late Friday. Hope that it finishes by Mon morning ... if your site is large and contains 'dead wood'.
Create a System Admin category and course in the 2.6 and in that course setup a file system repository which points to the m22backups autobackups or IS the m22backups. Use that course for restores to other categories, which have to be created before restoring IF you'd care not to have to move them later. A file system repository also keeps the backups (which you, I assume, will use only once) out of the new file system ... which will be bloated otherwise.
Then the game is choosing the correct m22backup to restore and re-assigning teachers in the course.
There's work to do in any direction. But that's why you make the big bucks, huh? ;)
'spirit of sharing', Ken