I want to import a 3GB system file to ELK in one go

As the first few fields are not in Kv format you can not just use a KV filter. Instead you need to parse out the fields that are not in KV format first and store the long KV string in a separate field. You can then apply the KV filter to this field. Have a look at this blog post for a guide on how to parse data and work with Logstash.