Removal of the head liner can be tricky - there is a lot of spray adhesive on the edges which tends to rip the fabric. I've seen new headliners advertised for about 100 euros over here...
...the problem is that there's a fair amount of foam between the head liner and the metal - that will be wet and still smell like the mice.
If I were you I'd go for the headliner removal and see if it will come out in one piece. Then do a replacement sun roof tray.
It seems like you are putting in a lot of effort to the car - it would be a shame to silly-cone the roof shut - see what Mike D has to say about silly-cone here =>
http://www.peachparts.com/shopforum/body-repair-restoration/339888-w114-rocker-panel-repair.html