Go for mySQL. Once you have your data files normalized into flat tables, loading them into mySQL will be really simple.

But take your time in working out the table design, in order to make it fully normalized -- e.g. although you have just two data files, it looks like you may want at least three tables: one for companies, one for the "datafile1" records that relate to those companies, and the third for the "datafile2" records. The nature of the "other text content" in your data files may suggest other relations that could benefit from being indexed/related via one or more additional tables, apart from these three.