My recommendation is that when you upgrade this far, you have an opportinuty for making the changes that your users have been looking for, so do a net new install of 12.1, apply your customizations, add any new features. You also have to figure out do you want to migrate the existing data or start new. Only your organization can decide, but there are benefits to both.
I would spend a lot of time planning, testing, but first installing 12.1 and understand the nuances, Also, develop and training plan for the features that have changed, new features, and enhancements from your company. Training is one of the key elements to making your users happy. If you are not already on Business Objects, plan on developing your reports. You can do some very good reporting in WEBI, and it does not take much time.
Also, engage a consultant that understands Clarity and the organizational impacts of this sort of upgrade/migration. They can be from CA, Digital Celerity, independant, or other. There are a lot of good consutants out there, and a good one will help you be successful.
In a nutshell, to be successful you need planning, planning, planning, testing testing, testing, and training.
If you have any further questions feel free to contact me:
tmlt@rogers.com
Good Luck!