If you compute the cost/hp for any given case it just doesn't make sense (especially in a small system) to re-rack anything that already has a case and power (lots of discussions on here about that). I would consider swapping the two passive mults with a mutable links, you get a 1:3, 1:2 (sum or mult), and a 3:1 mixer in 4hp. If you need more passive mults consider getting stackable or those knuckle splitters.
There are many i/o modules, I happen to use the 4ms i/0 has both an input and output section (that supports headphones). I am assuming the two pico outputs is an oversight.
I also use the Joranalogue Fold 6 (great wave folder in 4hp). I am not familiar with the uTune, or the BBD, but I would consider replacing the BBD with an FX aid XL you get a lot more effects for the money and when you settle on which effect you use the most you can get a dedicated replacement for that algo and try more of the available options (once you expand to a bigger case and you will expand if you keep at it).