After weeks of try and error, I think luckily I have archived what I wanted. Not 100% but to an acceptable level.
100% is to copy everything. Users would not even notice that it is moved. But that was not possible. I could not figure out how after all. The thing missing is user permission. That, I think I would re-setup manually. At least the admins. Then ask them to deal with their colleagues.
First, I write about the method that did not work for our site after all. I believe that is due to something particular with our site, which I could not figure out. I may have achieved the 100% if I could.
You copy the site to your new 2008 R2 server using msdeploy tool. http://learn.iis.net/page.aspx/427/migrate-a-web-site-from-iis-60-to-iis-7/
You activate (“extend”) FPSE (FrontPage Server Extension) on the copied site.
At this point, you realize that the FP user permission are missing. This is what you should do: http://blogs.msdn.com/b/robert_mcmurray/archive/2009/10/12/migrating-fpse-roles-between-servers.aspx.
In case your site is simple enough, this is the end of the story. You have achieved the 100%. However, with our site, the server health check repair did not work. It ends with an exception, without telling me what it does not like.
Giving up to copy the permission, I uninstall FPSE once then re-extend. Failed too. Stuck...
Here is the workaround that I found. I cannot activate FPSE on the fully copied site. Let us then have an empty FPSE enabled site first, and then pour the actual site data into it.
I created a blank web site, activate FPSE, and finally copy files from the old server with the following command.
msdeploy -verb:sync -source:metakey=lm/w3svc/1551257136 -dest:metakey=lm/w3svc/2,computername=newserver -skip:objectName=dirPath,absolutePath=.+_vti.+ -skip:objectName=metakey,absolutePath=.+vti.+ -skip:objectName=metaKey,absolutePath="fpexedll.dll"
The “-skip” parts are my invention. No documentation found. They are to not to copy FP related stuff. It looks work. All webs are copied, seem working. I can create FP web on them.