I have just finished an upgrade just like the one you described, except we did not use 64bit HW. We went from EV 5.0 on and older server to 2007 SP3 on new hardware/SAN.
The process I used which worked well, was to upgrade sequentially, like you described, to 2007 on the old server. We were running Server 2000 on the old box and 2003 Standard on the new. You will have to upgrade Outlook and maybe one or two other components on the way to make sure they are compatable with the newer version.
Once you get the Old server to EV 2007, I would build the new server, just not config EV. You will need to stop the EV services on the old server and then copy (Robocopy works well) the indexes, shopping and vault store data to the new server. If these are SAN volumes and they can just be reattached, great. The trick is making the data is in the SAME locations as before. So if your Indexes were on a E:\ drive, the index location should E:\
One important note on the sequential upgrade, backup your EV databases before each step. Back them up now before you begin, upgrade to 6, test and back them up again. Rinse and repeat. This way if you need to stop and go back, you have a clean DB to go to. I highly stress you test in between upgrades to make everything is working.
Once the old server is on EV 2007 and all the data has been copied/migrated to the new server, rename the old server and shut it down. I also like to disable the EV services from starting on the old server before shutting it down. Rename the new server the old server name (the CNAME or Vault alias should still point to the old name and work fine). Now the NEW server has the old name and IP and the vault alias still points to it. (I know simply updating the alias CNAME entry should fix this, but I have seen where 5.0 still embeds the physical hostname in the config in SQL and the recovery fails - I prefer to play it safe and rename the server and keep the CNAME as is.) Make sure all the data is available in the correct locations and run the EV config util.
Select create a new site, enter the VSA credentials and then on the next screen enter the SQL server (this needs to be the same SQL server as before). It will recognize the EV server as the old one and automatically start the recovery process and restore all the settings, policies, tasks and services on the new server.
At this point you should have everything up and running on the hardware.
In a nutshell, you are upgrading the EV first then walking through doing a DR/recovery on the new hardware.
I have done this a couple of times now and it works very well.
Hope this was helpful!
