I have been trying to run this query as recommended in the neo4j google group and in other sources online:
START n = node(*) MATCH n-[r?]-() WHERE ID(n)>0 DELETE n, r;>
You could increase heap space in your neo4j properties and enable gc log and watch the rise of heap space if it really near the upper limit.
page cache size needs to be reduced or increased depending on your initial size. ...reduce/increase it and check effect on load time.
neo4j is memory hungry... need bigger heap size as much u can get.