While you may have booked them at the same time via Kiwi, the two flights are actually ticketed separately and completely independent.
If you missed your second flight because you were denied boarding on the first, you have to complain to Kiwi about that second flight, though I wouldn't hold my breath (they will probably tell you you would have needed to get in touch with them within 5 minutes of being denied boarding to be eligible for anything, or something similar). Do ask them, though, you never know (the result may depend on any optional services you bought at the time of booking).
For the Wizz Air flight:
- You were owed the choice between a refund, re-routing at the earliest possible opportunity, or rebooking at a later date
- If you chose a refund, that stops there for this choice, and that covers only the Wizz Air flight
- If you chose re-routing, it would be to Sofia, which probably wouldn't have helped you much, as you probably still would have missed the Ryanair flight (though I have no idea what time it was supposed to depart on that date).
- And I suppose you didn't pick rebooking at a later date.
- You are owed compensation. However, only the Naples-Sofia trip would be counted, and that's 783 km, so you would be owed 250 euros (less than 1500 km), not 400.
So in total they owe you:
- The refund of your Naples-Sofia flight
- 250 euros
You have to ask the airline first. Check the "my booking" page on their site first, otherwise use their claim form.
Only if the airline does not respond within 2 months after you have sent them a claim (or if they refuse it) can you lodge a complaint with the Italian national authority (since the flight departed from Italy). Details can be found in this document.
Make sure you make it clear you want a cash refund (paid by bank transfer), not vouchers or credits or whatever else (unless you plan to fly with them again very soon).
They may make it difficult to pay you on a non-EU bank account, and it will probably cost you a bunch in fees from you bank to receive that payment.
Advice for next time: do not book with Kiwi or any other agency which sells "self-transfers". If you had booked an itinerary as a single ticket, the airline involved would have had to get you to your final destination (Berlin), at the earliest opportunity (i.e. the same day, even if that means rebooking you on a different airline) or would have had to pay all your costs to get there (under comparable conditions). Here their only obligation was to get you to Sofia, which wouldn't have helped you much.