Since you're staying with 2008R2 (both source and destination) there is nothing stopping you from just backing up and restoring all of your databases including the system databases. As Shanky pointed out, this would save a great deal of time:
1) Backup and Restore Databases - Is this the best option?
It's an option. If you need the downtime to be less, you can use mirroring or log shipping (or do it by hand) to keep the databases in sync and then migrate during a fast downtime or cutover.
Please note that system databases cannot be log shipped or mirrored and would need to either be frozen or copied right before the cutover.
2) Migrate Logins - use Microsoft KB? kb/918992
If you restore the master database to the new instance, no migration should be needed. All server level logins are stored in the master database.
3) Migrate Credentials/Certificates - what is required for this?
If this is inside of SQL Server, these would be held in their respective databases (and possibly master as well). The one difference would be the service master key (SMK) that would change. You make want to back that up and restore it on the new server if you're relying on automatic key decryption.
4) Migrate SQL Server Agent Jobs - (Object Explorer Details > Select All Jobs > Script Job; Is this process the best option?)
If you restore the msdb system database, all agent jobs will be held in it. There would be no need to script->restore.
5) Migrate SSIS Packages - (How to do this?)
If the SSIS packages are on the filesystem (not default) it would be trivial to create the same location on the new server and copy. By default the SSIS packages are held in the msdb system database and restoring it would get you to the same place, just like #4 and previous.
6) Migrate Database Mail Accounts/Profiles - (Create a script or recreate in SSMS?)
This is also stored in msdb. See #4, #5.
7) Recreate assemblies
These live in their respective databases. If backup and restore is used, this should not be a problem. Any assemblies outside of SQL Server would need copied to the new server.
8) Recreate Linked Servers
These also live in the master database, see #2.
Thanks to Aaron Bertrand, I was able to resolve the issue following the manual steps outlined in his blog:
...in spite of the title, it's not just for 2008 R2 or Evaluation Edition.
In case the link ever stops working, the essential steps are:
Locate SQL Server related GUIDs under:
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Uninstall\
Also look for GUIDs in folders under Uninstall called e.g. "Microsoft SQL Server 2008 R2"
Run for each item:
msiexec /x "{guid}"
Best Answer
thanks for the reply. The migration tool generates a report. In it's report, the migration tool listed SSIS as a feature that had to be deleted, it also indicated all maintenance plans had to be deleted. SSIS afaik was not installed and did not show in the features when I checked programs and features. This confused me. I had left the maintenance plans on while running the tool since we needed them. On a hunch I deleted the maintenance plans and SSIS was no longer listed in the report as a problem feature. The maintenance plans were backups, either they used SSIS somehow even with it not installed, or the MS's migration tool was wrong. In any case, with the maintenance plans delete I no longer have the problem.