Hi Lincoln Hood - I have done this analysis before when I was working in the maritime industry. So, let's break down your question as there's several items in there:
1. The files .cpg, .dbf, .prj, .shp and .shx which you mention are the components of a shapefile.
My first suggestion would be to import those shapefiles into a file geodatabase, it'll work quicker and it's easier to manage.
2. You suggest that you want to filter the data by timestamp and craft_id...this would involve combining all the feature classes (those shapefiles you imported to feature classes in a geodatabase a moment ago) into a single Feature Class (use the Merge tool) this will mean in a single database you will have all records in a single table, perhaps put this Feature Class in another File Geodatabase - you'll potentially end up with a large database but it'll be easier to work with for this analysis.
3. Filtering the database can be added to an ArcMap session as a layer. In layers you can apply definition queries. Use definition queries to filter out your data for example: Craft_ID = 123 AND Time_stamp > 01-01-2012 <=01-01-2019...Using the filtered layer you can run the below tools to end up with outputs for the filtered data. Of course, you could run these tools over the whole dataset but it'll likely take some time.
4. Converting the point data to lines try using the Points to Line tool...and the Craft_ID as the Line Field and the Timestamp for the Sort Field...let me know if that works, you should end up with lines per Craft_ID sorted by Time...this might take some time given considering the quantity of data...with the result you should have an approximate route for the vessel.
5. Once you have the lines you can use Line Density or the Calculate Density tool (you could also use Calculate Density tool with the points directly which might superseded the need for creating lines if the density of points are as required). There are various other density tools which maybe more appropriate like the Kernal Density tool but you'll require the spatial analyst extension for this.
It'll probably be easier if you have any questions on the above process to email me: skettle@ggspatial.co.uk