I've noticed a significant omission in the .dm file for the mod:
The mounted units lack the
#mounted command signifying they are mounted troops. I found this out when I saw that my Daimyo had a foot slot, and mounted commanders aren't supposed to have feet slots. You will also need to adjust the base
enc for both units upwards to a value of 5 (currently they are set to a value of 1), as per the mod instructions (section 6.29 of the doc), in order for the units to have the correct enc values.
I edited the Version of the mod that I'm playing with to test all the suggestions I've been making, along with those that Potatoman was making himself, and so far they seem to make things considerably more balanced, at least as far as my present engagement with Ulm (currently on turn 23). I'm an impatient gal and I didn't want to wait for the next mod Version.
My genin are a fair counter to Ulms HI. The samurai pin them in place from the front and the ninjas hit the HI from the rear, while other ninjas go after enemy archers. Ulm counters my ninjas by shredding them with missile fire as they move. Ninjas are remarkably vulnerable to archery, which really shouldn't be surprising. Given that the ninjas now cost almost 3x a samurai (in gold), you definitely feel the loss of each one. Which should discourage folks from just making ninjas when they should instead build "combined arms" forces.