In addition to posting on OGR Forum, I also reached out to Lionel. They responded promptly with their recommendation on a remedy to resolve the clogged water tower. The following response is from their maintenance manual:
Maintenance of your Water Tower Because your water tower uses water as part of its functionality, there are a few things that you will need to keep in mind. Firstly when using water to fill your water tower, always use distilled water. Using distilled water will help to prevent minerals from forming deposits inside of the tubing or pump. When storing your water tower, we recommend that you remove all of the water from the tank. This will prevent anything from growing or living inside your tubing or pump. After you remove all of the water, we recommend that you clean the tank thoroughly with warm, soapy water. You can use any standard dishwashing liquid. Do not add the soap directly into the tank of your water tower. Mix the soap with the water before you add it into the tank. Then simply cycle your water tower a few times to clean out the tubing and pump. You may want to also clean out your tank when you notice that some of the water you initially added is gone. The water colorant has some ingredients like sugar, and when the water begins to evaporate, the sugar will begin to re-crystalize. Using the soap solution to rinse out the tubing and pump will clean all of this out.