I think some of the smallest and least expensive items on your list of improvements are some of the ones that will give you the most enjoyment.
I would first get a Logitech Harmony remote. All you should need is a 550 model, which you can get for only about $75. You will love it.
Second, I would replace your sub. I highly recommend HSU Research, but just like speakers, there are tons to choose from.
The cooling fans are a good idea. A company called Cooler Guys sells some fan kits which you can easily install into the back of your media cabinet.
http://www.coolerguys.com/840556082491.html