Per the implementation of the TaskTracker instrumentation plugin implementation (from 2008), a ClassNotFoundException during loading up of an configured TaskTracker instrumentation class shouldn't have hampered TT start up at all.
But, there is one class-fetching call outside try/catch, which makes TT fall down with a RuntimeException if there's a class not found. Would be good to include this line into the try/catch itself.
Strace would appear as:
2011-08-25 11:45:38,470 ERROR org.apache.hadoop.mapred.TaskTracker: Can not start task tracker because java.lang.RuntimeException: java.lang.RuntimeException: java.lang.ClassNotFoundException: org.apache.hadoop.mapred.CustomInstPlugin