This is reposted from Kinzen's thread on shugenja/magic restructuring. My own version was considerably less ambitious and was more of a modified version of 4e systems already in place. This is still, very much, a work in progress and many of the techniques are in a heavily rough draft form but just in case I never get around to finishing it I figured I would post what I have "done" at the moment.
Spells
All 4e spells still existed in their current state, but were no longer selected by shugenja. All shugenja have Sense, Commune, and Summon. Sense now senses elemental kami specifically rather than examples of the element. Commune is used to both commune and to importune (as per the rules in the core book). Summon now allows you to physically manifest the kami which takes the form of the spell you importuned. In effect, Summon adopts all the qualities of the spell you're casting (Mastery, Range, Area, Targets, etc.).
Kami
Kami are a touch rarer in this system and are now part of the spiritual landscape that a GM should consider as part of their game. Kami have ranks 1-6 and can only be importuned to create spells of their level or lower (i.e. a Level 3 Kami can cast ML 3 spells or lower). Commune and Summon have a TN based on the personality and power of the spirit, using the following as guidelines:
Personality
1 - Helpful
2 - Friendly
3 - Neutral
4 - Unfriendly
5 - Hostile
Power
1 - Small kami (large rock, koi pond, breeze, camp fire, etc.)
2 - Minor kami (boulder, large pond, bonfire, etc.)
3 - Large kami (hill, small lake, stream, grotto, etc.)
4 - Major kami (river, mountain, large lake, minor nemuranai, etc.)
5 - Great kami (mountain ranges, plains, wildfires, major nemuranai etc.)/Celestial Spirits (Ryu, Fushicho, etc.)
6 - Fortunes and Dragons
Add the two numbers corresponding to the kami together then x5 (example: a small (1), helpful (1) kami would be a TN 10, while a Hostile (5), Fortune (6) would be a TN 55. As AtoMaki thought up, you can use the Commune spell to speak with these spirits and possibly shift its mood. This uses Spellcraft as a social skill similar to Courtier, Etiquette, and Sincerity. Summon is then used to channel or manifest the power of the kami to various effect roughly able to importune spell effects equal to or lower than the spirit's power level, and taking 5min per mastery level. After that the shugenja may 'hold' the spell for 1 hour.
Schools
The schools more or less stayed the same in terms of skills, honor, etc. but now had 5 technique (many of which were modified versions of base abilities, new path and advanced school techniques.
Yoritomo Storm-Priests
Rank 1: Child of the Sea - The family line of the Yoritomo who possess the talent for magic have a strong bond with the sea and with weather as a whole. You may expend one spell slot to alter the wind conditions in your current location by one degree. If you also spend a Void Point, you may instead shift the entire weather status one degree (see sidebar in Great Clans). You may expend a maximum combined total of spell slots and/or Void Points equal to your School Rank each Round to enact these shifts. These shifts affect an area a number of miles equal to your School Rank in all directions from your current location. You may cast the spells Sense, Commune, and Summon
Rank 2: Strength of Suitengu
You may spend a Void Point to release a lightning bolt from your hands as a Complex Action. This bolt strikes one target within a range of 30' x your Water Ring. It rolls and keeps a number of damage dice equal to your Air Ring. You may expend spell slots to increase the damage of this bolt by +1k0 per spell slot expended, up to a maximum of your School Rank.
Rank 3: The Raging Ocean
Your Water Ring is considered 2 ranks higher for purposes of determining the number of spells you may cast per day.
Rank 3: Child of Osano-Wo
You may spend A Void Point as a Free Action to gain immunity to all spells possessing the Thunder keyword for 3 rounds (including damage from techniques of this school).
Rank 5: Thunder's Call
You may use your Rank 2 technique to summon 2 bolts that may strike the same or different targets. Extra spell slots for damage on that spell award +1k1 per spell slot instead of +1k0 (and effect both bolts).