In many places within the parsers Java arrays are used as a type safe container

With Java 5 this is no longer a requirement to obtain type-safety for containers.

In addition the code complexity with explicit array allocation, etc, is often obscuring a method's intent.

My suggestion would be to try to eliminate all unnecessary usage of Java Arrays.

Potential change in performance could result (both faster or slower), depending on how the Arrays are used.

e.g. a hashed- or sorted container might search much faster than a linear search, if the array tends to be large

re-allocation of an array if its size is too small or too large could also be a problem.