The issue that you describe is the one that we reported to Joomla in january 2014 and that they still didn't fixed.
We have published a document in "Migration Jooml" (french)
/en/documentation/migration-joomla
See page 31
Aplly the procedure described in the Bugtracker
joomlacode.org/gf/project/joomla/tracker...racker_item_id=33177
In fact the problem is that under J3.x, when a DB error occurs, the process is immediatelly stopped and does not give the opportunity to fix other stuff.
In J2.5, such kind of problem does not occurs because it run all fixes and does not stop at first error.
This is a regression bug between J2.5 and J3.x that we reported.
Everybody agree that this should improve the process but Joomla didn't included it yet.
Before doing the upgrade to J3.x, we also strongly recommend that you start from a J2.5.28 because a part of the bugtracker that concern the J2.5 is included in J2.5.28
The problem concern the J3.x that still does not contain the fixes.