Databases are good at this sort of thing. And these come in all sizes and shapes. Free and commercial.
These do require you to think of a structure for your characters, structures for locations, etc. Later when all that info is stored, you can use JOIN's, indexes and such to create the whole picture. That is what you have to do with relational database server software and the SQL query language. Free/open source database software you could opt to use: MySQL, PostgreSQL, Oracle Express (10GByte limit), Microsoft SQL Server Express (10GByte limit). That are the most common ones and you can find lots(!) of information and tutorials for these and are available for most, if not all operating systems. Does your data exceeds the limit of either Oracle or Microsoft over time? Then it will be time to fork over pretty serious cash for the Microsoft product or get bound over a barrel with Oracle. But if you don't, their products are pretty nice and relatively easy to work with.
There are also a different form of database, generally known as NoSQL database software. These are great for collecting data in a less structured way. These are more often than not open source and have a community version available. Also enterprise versions, but these can be just as expensive as Microsoft/Oracle products. These often do impose limits on the operating systems they run on and you'll get better support on Linux or Mac then on Windows. The included client software support for Windows is usually sparse/spartan and 3rd party products that allow you to work properly is costly. Databases to consider here: MongoDB, Cassandra, CouchBase.
What will be a major pain though, getting the data from your Excel, sheets and EverNote into any of the database of your choosing.
Some 10 years ago I inherited a MediaWiki installation and I am maintaining it ever since. In my opinion it is great for making documents that don't require much alterations afterwards, such as manuals. But for keeping track of data, not so much. Not sure if is just MediaWiki, but the interface that comes standard with it is horrible. Unless you are are very well versed in the syntax of MediaWik, it is workable. If you're not, you might even call the interface disgustingly bad to downright evil.
Relational databases scale pretty well, NoSQL databases scale very well.