X5540 is apparently a very good choice keeping in view your concerns however if you are also concerned about your budget, you can scale down to X5530 which runs at 2.4GHz and would equally serve the performance but save you more than $200 (depends on the pricing you are getting in your region).
As for overclocking the cores, you can disable and enable individual cores based on your application requirements and the cores can be overclocked giving you higher performance gains over it's native speed.
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