I cleaned mine over the winter. Since I couldn't find much information about how to properly do it, I just "winged" it. I was worried about muriatic acid being too aggressive so I used a product similar to "CLR" from Home Depot. My heat exchangers only open at 1 end, so I poured the stuff in and used a stiff wire to carefully "rod out" the tubes. Lots of bubbling told me it was working. I poured it into a bucket and then back in 2 or 3 times and was able to re-use about 50% of the stuff for the other heat exchanger. I flushed/rinsed them thoroughly and put in new gaskets. Make sure you don't tighen down too much- the gaskets work best snug, not tight. Before re-installing them they both got sanded down and a fresh coat of paint. I guess I did a decent job because they worked like new when I fired the engines in the spring.
Hope this helps.