Here is some additional reference info on conditional value lists. It includes the link you have already found but the last link should be of particular interest to you as it spells out how to set up hierarchical conditional value lists. In otherwords, the value you select in field 1 controls what values appear in the value list for field 2, then when you select a value in field 2, this will control the values listed for field 3 and so forth...
There's a lot of overlap between the first two links so you can read one and skim the other. The demo file gives you several examples of different conditional value lists so you can examine them to see how they are set up. If you are using FileMaker 12, you can open this demo file from your File menu to get a converted copy of the demo file that you can examine in FileMaker 12.
The last link discusses how to set up a chain of conditional value lists where the value selected in each conditional value list controls the values listed in the next value list.
Forum Tutorial: Custom Value List?
Knowledgebase article: http://help.filemaker.com/app/answers/detail/a_id/5833/kw/conditional%20value%20list
Hierarchical Conditional Value lists: Conditional Value List Question
For your Hierarchical conditional value lists, you can set up multiple table occurrences of Master Taxonomy, each linked to Database 2 by a different match field pair in order to get your different value lists to work.
Feel free to post follow up questions here if those links aren't enough to get your value lists working correctly.