I absolutely LOVE my Vitamix and now I want to go smell the containers! LOL I have the regular container and the "dry" container. I went and smelled them both along with the two-part lid. They smell like clean air, so I can vouch for our cleaning method.
After emptying contents, rinse with hot water and fill just a hair above the 5 cup mark. Add a drop or two of dishwashing liquid. After putting the lid back on, put container on Vitamix base and run for 30 seconds. This creates a nice sudsy cleaning whirlpool bath! Pour sudsy water out of the small hole (leave black lid in place) into the small lid. Rinse all parts in hot water and let air dry. BTW, the full rinsing/washing/rinsing process takes me about a minute and a half and I don't use a lot of water...just enough to swish and swirl around. I also use the freshly made hot sudsy water to wash something else in.
Anyway, be sure to store the container without the lid on. I store the containers on their sides, so that moisture can escape easily.
Now... to get rid of the disturbing smell... I would try the following methods one at a time until something worked:
~ Wash as I described above several times over the next few days (as you wash regular dishes, so you can use the wash water). In between washes, after it is fully dry, sprinkle with baking soda to absorb odors.
~ Grind up an orange in the Vitamix...whole orange (leave peel ON, but wash it first if it is not organic) cut into a few pieces (3-4) and let it sit there for a few hours. Then wash as I described above.
~ Something my MIL suggested to me when we first moved into our house and had the previous owners very strong spice odors lingering forever in one of our cabinets is to place a small dish of vanilla extract in there. IT WORKED! It took a long time, though. Adapt that idea, perhaps
I don't know what CLR is, but if it is a chemical of some kind I would consider that container an expensive lesson learned and destroy it and buy a new container. I would suggest making compost in it, but it really depends on what kind of cleaner it is.
Bottom line, though, is figuring out what caused the smell in the first place and eliminating that from the process.