You should have a look at the --reference option for chmod:
chmod --reference version2/somefile version1/somefile
Apply find and xargs in a fitting manner and you should be fine, i.e. something like
~/version2$ find . -type f | xargs -I {} chmod --reference {} ../version1/{}
This even works recursively, and is robust against missing files in the target directory (bar the No such file ... errors, which can be ignored). Of course it won't do anything to files that only exist in the target directory.
Cheers,