Do following step will be best for any weblogic portal upgrade.
1) Create a new portal project and copy manually all your source files (java,jsp and portlet).
2) if you are using validation xml then put that in config folder available under web content (not remember its available by default or you need to copy from Merged project).
3) if you have any specific filter / weblogic application xml changes then you need to do that manually.
4) at any point of time any upgrade option will not work.
5) update with latest version of jar your ant/maven script
Hope this helps