I just did the same to a PI dual stack 7.31,
Lessons learned. I wanted to avoid using SUM tool. So i built my XML package with MOPZ in SOLMAN, loaded the ABAP stack via SPAM, then went to load the Java patches via JSPM.
JSPM had a patch, updated it, restarted and told me JSPM is no longer supported. I had to go back to use SUM.
Now when running SUM, you will need to start it with a -java only switch. Problem is, your XML document will contain info for ABAP, yet ABAP is already patched..
I had to regenerate a XML again only for my JAVA stack..
Long story short...just use SUM for both stacks.
Also, I thought SAP discontinued dual stack support as of 7.4? Only SOLMAN is supported.
??