My honest reccomendation:
1. Keep it stock, or find a OE replacement for the sub if its broken.
2. Replace the box, amp, and sub.
I say this because the box doesnt do well with larger/stronger subs and amps. if you are going to upgrade, you need to do all 3 at once.
Also, I recommend upgrading your headunit before any of this, that will give you the best boost in sound quality.