I took a look at the PSDs to see if I could contribute too but it looks like I'd need a long time learning to maintain that style and quality you already have - it's very good.
If I could venture some suggestions, these would be the things I'd like most and that I think might be prioritized:
*Simple UI and Interface improvements.
-Improved clicking. Right now, actions done by clicking register on the Mouse-1-Up (release of left click) only if cursor hasn't moved since Mouse-1-Down. If you click and drag even one pixel before releasing, the click does not register. It's inconvenient in practice, especially with big herds and you are rushing to get things done. Maybe make it activate on any object or coordinate under the cursor on Mouse-1-Up regardless of where the cursor was when Mouse-1-Down was pressed.
-Sweep All Plates & Sweep All Poop buttons; While clicking constantly is how some games keep players engaged (like Farmville), I think it's worth considering this.
-Unify Sweep and Clean; have a single tool that will sweep poop and plates and clean yukkuri.
*Barriers; some simple straight line way to divide the yukkurarium into sections as a precursor to adding physical passable/impassable objects.
*Accessory-less yukkuri tolerate each other; I found it strange that they would lament their missing headpiece and lambast others for lacking it in one breath. Maybe as a precursor to a more complex "Opinion_Towards" system where each yukkuri can generate an opinion or attractive/repulsive rating on other yukkuri based on accessory, type, deibu-ness, cleanliness and so on.
*Permanent Surgeries: (IMO they should be permanent in the game context even if they might be fixable canonically)
-Burn feet; Stops that yukkuri's movement as a second method to control. The graphic would be simple. Right now they will all die of hunger but ways of saving them can be added later.
-Castration; Stops that yukkuri from breeding. No graphic needed.