You could use this script (it changes the permissions recursively but individually for each file/directory)
#!/bin/sh
chmod --reference $1 $2
if [ -d $1 ]
then
if [ "x`ls $1`" != "x" ]
then
for f in `ls $1`
do
$0 $1/$f $2/$f
done
fi
fi
Run the script with arguments version2 version1