The title is a bit weird as I\'m having difficulties narrowing down the problem. I used my solution on Hadoop 2.0.0-cdh4.4.0 and hive 0.10 without issues.
From what I've seen, Hive-.11+ has a bug in join with custom SerDe.
https://github.com/Esri/gis-tools-for-hadoop/issues/9
You might try the workaround of copying the JAR file containing the SerDe class, to $HIVE_HOME/lib .
(I see in your question you got ClassNotFoundException both in join and in other cases; so far the times I have encountered such were all with join.)
[Edit] Another workaround is to use HADOOP_CLASSPATH:
env HADOOP_CLASSPATH=some.jar:other.jar hive ...
[Edit] The work around applies to Hive versions 0.11 and 0.12; then 0.13 and above contain the fix for HIVE-6670.