Using the library manager you can do it. After pressing the browse button a file browser opens. In it you can use shift plus leftclick to make multiple selections. (crtl plus left click also works if you want to have more control.)
Footprints work exactly the same. 3d models do not need to be imported. Just store them wherever KISYS3DMOD points to. Or if you have personal footprints that use them, setup your own path variable.
Depends on the exact files. On their scaling and how the footprint intended to use them is setup.
A lot of version 4 footprints had a scaling factor of 1/2.54 set in the 3d model options. We now do no longer allow the use of this scaling factor in the official library. This means all footprints are now setup to work with 1:1 scaling now. (This means the footprints expect the 3d model to be scaled 1:1)
If your own 3d models are not scaled that way you will either need to correct them or make your own footprints that define a scaling factor.
Might just be that the footprints now have a slightly different name. (P2.54mm instead of Pitch2.54mm for example) If this is the case then you will need the old 3d model lib for v4 projects and the new v5 3d model lib for new projects. (“Simply” switch the KISYS3DMOD variable depending on which project you currently work on. Sadly there is no way to define this variable for a project so you really need to either manually switch it or use batch files for setting up kicad with v4 libs while working on old projects. Another easy option is to run kicad setup for v4 libs in a vm for maintaining old projects.)
Not directly. but you can add a 3d file per color and manually assign it in pcb_new. Or make a footprint per color.
Did you try to refill the zone? (Shortcut “B”)
Kicad does not allow for orphaned fills, is it possible that your design had such orphaned zones?
Is it possible that the zone settings are different then originally in eagle (min width setting and clearance setting.) If this is the case then the importer did screw up and you could raise a bug report about that.