I know that upgrading from R6.5.x to R9.0.1 (in one step) is not supported by IBM.
IBM says:
"If you are running a release of Notes/Domino prior to 8.0, you should upgrade to at least Notes/Domino 8.0 before installing and upgrading to Notes/Domino 9.0. Upgrading from prior versions may work but is not tested or officially supported."
The steps would be:
1) update Domino Servers (1 Domino for Mail, 1 Domino for Apps with no web applications - only notes with @formula + LotusScript)
2) leave Lotus Clients in version 6.5 (about 1000 users), but update these in the next 4 months (I hope)
3) after migration, do not modify Notes applications using Domino Designer 9, only use Domino Designer 6.5 until ALL clients has migrated to Notes 9.
Thanks for the comments that can give me