You might get a temporary improvement by advancing innodb_buffer_pool_size to 750M.
> benchmarking this is a pain since results vary greatly
Automate unsetting the query cache ...
CREATE PROCEDURE `setquerycaching`( pcache bool )
BEGIN
IF NOT pcache THEN
IF @prev_query_cache_type IS NOT NULL THEN
SET @prev_query_cache_type = @@LOCAL.query_cache_type;
END IF;
IF @prev_query_cache_size IS NULL THEN
SET @prev_query_cache_size = @@GLOBAL.query_cache_size;
END IF;
SET LOCAL query_cache_type = 0;
SET GLOBAL query_cache_size = 0;
RESET QUERY CACHE;
ELSE
IF @prev_query_cache_type IS NOT NULL THEN
SET LOCAL query_cache_type= @prev_query_cache_type;
END IF;
IF @prev_query_cache_size IS NOT NULL THEN
SET GLOBAL query_cache_size= @prev_query_cache_size;
END IF;
END IF;
SELECT
pcache AS 'Query Caching',
@@LOCAL.query_cache_type AS QCacheType, @prev_query_cache_type AS 'PrevType',
@@GLOBAL.query_cache_size AS QCacheSize,@prev_query_cache_size AS 'PrevSize';
END;
If you have a Windows box, you could install 5.1 and 5.6 on it, optimise the 5.6 installation, and benchmark.