[shatner]

Well, the Shugenja is supposed to be a mountain hermit; he's even got mountain survival. That says to me earth and air. Furthermore, you mentioned earlier how important E2 and E1A1 is for the summons tied to those paths. As such, rather than have the Shugenja be E1 + 2xAEFWN (thus diminishing your chances of getting E2 and E1A1), we can change it to E1 + 1xAEFWN + 1xAE. That way you have a 100% chance of getting E2 or A1E1, and a 1-in-5 chance of getting either E3 or E1A2. That keeps them useful but still less magically powerful than the Master Shugenja. Since these guys are map move-2, they'll probably be your go-to mage for offensive battlefield casting (bladewind, legions of iron, destruction, lightning bolt, arrow fend, etc.).

For the Onmyo-ji... hmmm. You can make him younger if you'd like... it's a nice touch even though it has only the tiniest impact on their performance in-game. You could make them map move-2; that'd make a big difference between the MA and LA versions. Or you could give them recuperation and include some text about them recovering from non-fatal injuries quickly as a result of their near immortality. Other than Map Move-2, these are all minor changes but I'm not seeing a need to improve the Onmyo-ji in an important way, like giving them additional magic paths or flight. Having a recruit-anywhere 4.1 path mage (with a max path of 2) is about normal for the middle era.

As far as the Seigu, you'll have to map out the conceptual space you want that unit to fill before I can offer any further suggestions. If you want it to be a key player in communions, you'll need to make her a better version of the Onmyo-ji or do something neat like the auto-communion master/communion slave idea I had. If you want her to be something else... hmm, what are our options?
1) Mage++. Lots of nations' cap-only mage is just a better version of their run-of-the-mill mage. You can do something crazy like give her S2 + 1xAA/EE + 1xFF/NN/WW + 1.1xAEFNW. Boom! Instant, superior version of the Shugenja and Onmyo-ji. Make her old and/or map move-1 and you have yourself a reasonably balanced, high-caliber mage.
2) Super awesome researcher. Like LA Bogarus' Staret; lots of paths and a research bonus.
3) Super cheap. If you want to accept that MA Jomon is going to hire a huge pile of Shugenjas and/or Omnyo-jis then you can make the Seigu as good a caster as either but make her slightly cheaper AND sacred. Since you'll have Ryujin and summons to help reliably break into the higher tier spells, you can more easily get away with the cap-only mage being a magical light-weight but super-efficient researcher.
4) Thuggy. Give her good stats, helpful self-buff paths (air, nature, earth, astral), sacred + at least H1 and maybe stealth. Once your gem income and construction research comes online, hand her some gear and send her out raiding.
5) Special Spell Caster. Create some more of those five-sign spells but make them require H2 and A2/E2/F2/N2/W2 (and make her paths be H2 + 1xAA/EE/FF/NN/WW). Then when you want someone to cast the "wide scale air-shield, moral boost and lightning resistance sign", or the "remove fatigue and give reinvig-2 to a cluster of casters sign" you hire Siegus. Just make sure you make those new spells appropriately placed in the research tree.
6) Unit Spawn. Give her a summon allies ability that lets her spawn something worth spending a cap-only mage turn spawning.
7) Economy Boost. Give her abilities like fortune-telling, causes good events or lowers unrest. That way just having them around is passively boosting your economy.

There's more but that should be enough to get to brainstorming over.