I would suggest to remove half of the engines on the first stage: your TWR is way above 2, you don't need that much power. 2 Hawks will be way enough to lift that launcher, and having less engines stacked together will help to make room for your landing system.
The way you protect the structures with fuselage is well thought, though they are not fully shielded.
The second stage is simple but efficient, you can eventually consider adding a second kolibri to get more thrust, but apart from that it's good.