Cleon
Legend
Looks like a good start. You've left a couple of lines of Bugbear text at the beginning of "Houyhnhnms as Characters".
Going through the x's that remain:
Attack: I'd put the hoof damage at 1d4, same as a light warhorse, 1d4+3 once its 17 Strength is included. (Spiked horshoes do 1d6, armour spikes 1d8)
Skills: Autohypnosis, Jump, Listen, Spot, Swim, Survival?
Listen, Spot should definitely be among them as all the SRD horses possess those skills. Autohypnosis or Concentration, Jump, Swim and Survival seem appropriate as well.
Hey, if we give them Autohypnosis that would explain their resistance to fear, since they can substitute a skill check instead of a Will save. Then we wouldn't need the 'Brave' special quality!
Feats: I'm strongly tempted to give them Endurance and Run like a light warhorse, they do have all those "Exercise Races" for their children.
Organization: Solitary, team (2-20) or herd (10-100)?
Challenge Rating: 2, they're about as tough as bugbears.
Treasure: A bit tricky. Going by Swift's description they're not big on material possessions. No coins or gems, standard goods and items?
Alignment: Usually lawful neutral seems most fitting.
Level Adjustment: Around +2? They've got good ability scores across the board. There are too many exploits to circumvent their trouble wielding weapons for it to be worth a LA cut.
Size and weight: Well a typical horse is roughly 8 feet long and 1000-1200 pounds, that seems about right to me. A destrier or carthorse may weigh 1500-2000 pounds, but I'm thinking Houyhnhnm are not that heavy (except for the Schwarzenegger equivalents amongst them).
Special Qualities:
Brave: As I said earlier, how about dropping Brave and giving them Autohypnosis.
Darkvision: I know it gets this from being a Magical Beast, but a Houyhnhnm that can see in pitch-black conditions doesn't feel right to me. Could we drop it and just have Low-Light vision?
Nonproficiency: OK by me.
Skills
Should we have any racial skill bonuses? Regular horses don't have any. Maybe a +2 on Autohypnosis.