SQLite is a great tool to use as you migrate data from flat files. In fact I have been using SQLite for years for everything from config files to storing large data maps. There are so many tools for it and it is so light weight it is nearly as accessible as a human readable file but with a bit more kick.
That being said, and this is from my own experience - others may vary, just get your flat file data into SQLite however you find most intuitive to you (or your team) at first. In most cases the size of the data will be very small (relatively speaking in terms of DB performance) and the overhead of trying to learn SQL, Entity Relationships and all of the nuances of how to improve your DB performance are useless until you identify your database as being a performance issue. In many ways this is premature optimization. What you are doing is fine as long as you get the results you are looking for or at the very least get the same information you got out of the flat files.
Normalization of your database with foreign keys and foreign key constraints is tedious and time consuming to do correctly (once available the tendency is to lean on them which causes issues on it's own). Learning how to design, manage and run a database can ultimately lead you down a path to not completing your game. That is not to say time spent on learning the intricacies of database design, management and optimization would ever be a waste of time (I spend a lot of time doing this for work) however it will be a distraction from getting your game completed. Also in my experience, rarely has a database design been a bottle neck for any projects I work on until down the road when there are 1-3k+ users all adding and reading data at the same time. Granted the DB is almost always a bottle neck when we reach certain user thresholds or data sizes however at this point the applications are usually working well and the time spent on the database has more focus since the application has had time to mature and we know what kind of performance we are looking for.
I will repeat myself and say that overall I would do what is most intuitive for you and your game - especially if you are the sole developer. Database management has many religions and like any religion there are zealots who believe their word is Dogma and we all know how that turned out for Cardinal Glick. Once it is working for you the worst that can happen is you improve it.