can I run two versions of safari side by side
Unfortunately, Safari does not support multiple user profiles.

Even if you create a copy of Safari.app and execute it separately, both of them will load the same user profile which lies in your Library.

But, if your only requirement is the selective bookmark transfer, then you may export your bookmarks from your old machine as a html page, open that page in your new Safari, and selectively add the bookmarks as you wish.

In order to export the bookmarks, you just need to go to File > Export Bookmarks.. and then just open the resulting file from your new Safari.