Actually, you managed to nail the architecture as best as you could in this tiny a space, which is pretty impressive. However, if you plan to use this with a Beatstep, you might also look at Expert Sleepers' FH-2. This will need a 4 hp expander for 5-pin MIDI use...but if you went with a Beatstep Pro, then you could directly link to the FH-2 via USB, freeing up 4 hp for other uses. The FH-2 uses standard Scala format scale tables for microtunings, and offers a bit more freedom in configuration as the eight outputs are user-configurable. Plus, since it has four inputs for CV or gate, you can get the modular to "talk back" to the BSP depending on how the FH-2's been configured.
A better idea, though, would not only be to use the FH-2 instead of the Yarns, but to move up a bit more in size. An Intellijel 4U x 104 hp cab would not only let you use more than double the present 3U space for standard modules, you'd also have the 1U Intellijel-format tile row in which some other basic functions can be placed, such as I/O, a basic mixer, noise + S&H, mults and so on. The form factor would work nicely with the BSP if you went that route, also. Plus, you can put a 1U Zeroscope in that row, which has a tuner that displays in Hz...which, if you're doing tuning-critical stuff, would be majorly useful!