I've got spell lists for my three Maho-tsukai sub-classes, Onmyoji, Soryo and Yamabushi done (may switch a name here or there for color, but the list of spells is done), and descriptions of the spells for Onmyoji and Soryo are complete. Just the Yamabushi spells left to go.
I also have listed out Background Skills. Each class/profile gets a skill or two automatically, and then a number to select from a list determined by your character's social status. Kuge (nobility) don't have the same sort of background skills as Noumin (peasant farmers) after all.
Skills will work on a modification of the Turn Undead mechanic, or more or less like any sort of action in Presidents of the Apocalypse. Roll two dice (usually 2d6) and try to beat a 7, 9 or 11 (sometimes 5 for very easy things, sometimes 13 or even 15 for very hard things) depending on how hard the GM thinks it will be.
Shinobi special skills work the same way, although they start out with some skills at only 2d4, some at 2d6, and some at 2d8. The dice they roll also improve with level. And their special bonus dice (a replacement mechanic for Flying Swordsmen stunt dice) can be used to improve these rolls.
I've come to really like the "roll 2dX" mechanic, as it gives a nice weighted spread. Extreme successes are uncommon, but extreme failures are also uncommon. It's less swingy than d% or d20. Characters will hopefully seem fairly competent when it comes to skill use in Chanbara.
Still need to decide what to do about "unskilled" checks. A few background skills, like Astronomy/Geomancy, are the sort of thing you just can't do without training. But Fishing? Sure, anyone can fish, just not like a pro. I figure most of the time, the Background skills will not even need rolling. But when they do, and someone tries to do something that should be covered by a skill they don't have, what's the best way to do it?
Lowering the dice is one way. If Background skills are normally rolled on 2d6, then have the unskilled PCs roll on 2d4. That works, but then does that mean Shinobi with a 2d4 in a special Ninpo skill are untrained at it? Or just with minimal training? I can live with that, but some players might object. We'll see. I definitely don't want skills to be exclusive for the most part.
Also, I'm wondering if I should allow Ability Scores to affect Background Skills. The concern is that it would lead to stat inflation a la 3E/Pathfinder. My gut tells me to just stress the Background Skills are just that, the character's background. Now, you're an adventurer, not a poet or blacksmith or inspector. If someone needs something smithed, and your PC has that background, they can do it. Done, move on to the adventuring! It's only if the Hannya Queen demands an intricate cast iron puzzle be crafted or she will devour the village's children that it might be worth making a check to see if you can make one good enough for the snake-hag. [But even then, the players are still more likely to try and kick her butt rather than appease her, aren't they?]