Muriatic Acid won't leave a residue. I would suggest caution in using something like CLR though. While it is acid based like Muriatic, it also has some soaps in it that will leave a residue. Soaps are what are called "surface active compounds" and chemically bond with surfaces and have a tendency to leach back into the water for a long time afterwards. Most soaps can cause problems with a fishes gills. That's why we usually only recommend acid based products like vinegar or muriatic acid.

Certain bacteria are involved in the scale deposition procedure. They actually help scale deposits form. So, after you decalcify with acid, its usually necessary to clean it with a tooth brush. The same thing applies to coraline algae. After you remove the calcium, there is an organic residue left over. That's what I do when I clean my pumps. Soak it in acid first, then scrub with a tooth brush, then rinse real well and test the pump.

Pumps will usually scale up first. That's because the pressure change in the impeller cavity catalyzes the scale process. I try to clean my pumps every 3 months or so as part of my routine maintenance schedule. I have noticed a lot better performance from them by doing so. The trick is to remove the impeller from the stainless or ceramic shaft when you clean them. That seems to be the biggest problem. You may have to soak it for a while before are able to remove the shaft. A very small amount of scale on the shaft can cause a lot of problems in preventing the impeller to spin freely. If I need to get the pump back in operation quickly for something like a main return pump, I use muriatic acid. If its something like a maxijet that is not a main pump I will use vinegar. Its also a good idea to have spare impellers so that you can just swap them out and get it back in operation quickly. Then you won't be in a big rush to get it cleaned. Just let it soak for a few days, clean it, and store it until the next time the pump is due to be cleaned. Unfortunately replacement impellers can be hard to find and can cost almost as much as a new pump.