SSIS processing only 5000 rows from csv file to sql table
The source file shows only 5000 coming through from the first step. 

This means all of the data in the file got imported and there was a bad delimiter making some of the data get merged in the import or you have error notification / truncation notification turned off and the data was truncated due to destination or transformation constraints.

You could also have configured data rows to skip on accident or there are actually only 5000 rows of data. I'd start by examining the data, then looking into the logs. Make sure SSIS logging is enabled and look to the logs for more information. I would also add a count step between each of the steps and store them into a table for tracking so I can verify the amount of rows coming through each way.