Hi. I am wanting to run a userevent script when a file is imported via the "Make Journal Entries / Import" option. When doing a normal import you get the advanced option to run server suitescript but this is not available for the journal import option. Will as script run successfully using this method?

If you're creating (or editing for that matter) JEs then yes that will trigger UEs The only exception to this is when the thing that creates (or edits) the record is itself a user event based trigger. (this is to avoid "infinite loops" of UEs triggering each other)

We will be importing CSV files to create a journal entry. So, sounds like this should work.