Churches of Toril
Edena, as promised here is a list of the churches of Toril, minus the Mulhorand and nonhuman pantheons which should be taken as a group. I suggest that any unclaimed churches go to the weaker players.
Also, I think that the ability to move all of one's armies anywhere instantaneously is too powerful. I don't think even Netheril or the elven kingdoms of the Crown Wars had that sort of power. (12th level magic would have done it. Hmm, maybe Karsus should have researched THAT spell instead.

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Churches of Toril:
Note: I have adapted this from the FRCS, pages 234-241. Remember Edena must assign how powerful each church is and whether you may have it. However, I believe it is fair to say that the churches of deities of similar power, i.e. two lesser gods, should be similar. The ranks of deities are abbreviated as follows: Greater god (G), Intermediate god (I), Lesser god (L), Demigod (D). Remember, it is best to pick churches appropriate to your faction’s alignment, culture, and purposes. Thus, it would make very little sense of me to pick the Church of Bane. Or someone running the Orcs to pick elven deities. Notes reflect facts about the deity as they exist in the FRCS. This maybe subject to change by Edena.
A pair of parentheses after an alignment indicates an alignment tendency, based on what I know of the Realms. A question mark means I believe I am correct, but not absolutely certain. Thus, Finder Wyvenspur is CN (cg) Chaotic neutral with chaotic good tendencies. Hoar, god of retribution, revenge, and poetic justice, is LN in 3E, but I believe had some LG tendencies in 2nd Edition. Also, remember that clerics usually have to be in one alignment step of their deity. Thus, a priest of Tiamat may be LE, LN, or NE. A cleric can only be of neutral alignment if his deity is of that alignment.
In practical terms, Churches can help an underpowered player and the churches can help a player come up with a theme for his or her faction. It is important for a player to make sure that the interests of the churches he controls are at least respected, and better yet, promoted by a player and his country.
The format is Church, followed by deity rank, and alignment. Domains are in the next line down, followed in the line afterwards by portfolio. The last line are notes if appropriate. (It looked better in word.) Follow the example of Akadi below.
Church of Akadi (G) N
Domains: Air, Illusion, Travel, Trickery
Portfolio: Elemental air, speed, movement, trickery
Church of Auril (L) NE
Air,Evil, Storm, Water
Cold ,winter
Church of Azuth (L) LN
Illusion, Magic, Knowledge, Law, Spell
Wizards, mages, spellcasters in general
Serves Mystra
Church of Bane (I) LE
Destruction, Evil, Hatred, Law, Tyranny
Strife, hatred, tyranny, fear
Church of Beshaba (I) CE
Chaos, Evil, Fate, Luck, Trickery
Random mischief, misfortune, bad luck, trickery
Once part of Tyche
Church of Chauntea (G) NG
Animal, Earth, Good, Plant, Protection, Renewal Agriculture, farmers, gardens, summer
Church of Cyric (G) CE
Chaos, Destruction, Evil, Illusion, Trickery Murder, lies, intrigue, deception, illusion
Church of Deneir (L) NG
Good, Knowledge, Protection, Rune
Glyphs, images, literature, catography
Serves Oghma
Church of Eldath (L) NG
Family, Good, Plant, Protection, Water
Quiet places, springs, pools, peace, waterfalls
Church of Finder Wyvenspur (D) CN(cg)
Chaos, Charm, Renewal, Scalykind
Cycle of life, transformation of art, saurials
Church of Garagos (D) CN
Chaos, Destruction, Strength, War
War, skill at arms, destruction, plunder
Church of Gargauth (D) LE
Charm, Evil, Law, Trickery
Betrayal, cruelty, political corruption, powerbrokers
Church of Gond (I) N
Craft, Earth, Fire, Knowledge, Metal, Planning
Artifice, craft, construction, smithwork Clerics may be of any alignment
Serves Oghma
Church of Grumbar (G) N
Cavern, Earth, Metal, Time
Elemental earth, solidity, changelessness, oaths
Church of Gwaeron Windstrom (D) NG
Animal, Good, Knowledge, Plant, Travel
Tracking, rangers of the North
Church of Helm (I) LN
Law, Planning, Protection, Strength
Guardians, protection, protectors
Church of Hoar (D) LN(lg?)
Fate, Law, Retribution, Travel
Revenge, retribution, poetic justice
Church of Ilmater (I) LG
Good, Healing, Law, Strength, Suffering
Endurance, suffering, martyrdom,perserverance
A member of the Triad with Torm and Tyr
Church of Istishia (G) N
Destruction, Ocean, Storm, Travel, Water
Elemental water, purification, wetness
Church of Jergal (D) LN
Death, Fate, Law, Rune, Suffering
Fatalism, proper burial, guardian of tombs
Serves Kelemvor
Church of Kelemvor (G) LN
Death, Fate, Law, Protection, Travel
Death, the dead
Church of Kossuth (G) N(LN)
Destruction, Fire, Renewal, Suffering
Elemental fire, purification through fire
Clergy may be neutral or lawful neutral
Church of Lathander (G) NG
Good, Nobility, Protection, Renewal, Strengrh, Sun
Spring, dawn, birth, youth, vitality, athlectics
Church of Llira (L) CG
Chaos, Charm, Family, Good, Travel
Joy, happiness, dance, festivals, freedom, liberty
Church of Loviatar (L) LE
Evil, Law, Retribution, Strength, Suffering
Pain, hurt, agony, torment, suffering, torture
Church of Lurue (D) CG
Animal, Chaos, Good, Healing
Talking beasts, intelligent, non-humanoid creatures
Church of Malar (L) CE
Animal, Chaos, Evil, Moon, Strength
Hunters, stealing, bloodlust, evil lycanthropes
Church of Mask (L) NE
Darkness, Evil, Luck, Trickery
Tieves, thievery, shadows
Church of Mielikki (I) NG
Animal, Good, Plant, Travel Forests, forest creatures, rangers,dryads, autumn
Church of Milil (L) NG
Charm, Good, Knowledge, Nobility
Poetry, song, eloquence
Serves Oghma
Church of Mystra (G) NG
Good, Illusion, Knowledge, Magic, Rune, Spell
Magic, spells, the Weave
Church of Nobanion (D) LG
Animal, Good, Law, Nobility
Royalty, lions and feline beasts, good beasts
Church of Oghma (G) N
Charm, Knowldege, Luck Travel, Trickery
Knowledge, invention, inspiration, bards
Clergy of any alignment
Church of the Red Knight (D) LN
Law, Nobility, Planning, War
Strategy, planning, tactics
Church of Savras (D) LN
Fate, Knowledge, Magic, Spell
Divination, fate, truth
Serves Mystra
Church of Selûne (I) CG
Chaos, Good, Moon, Protection, Travel
Moon, stars, navigation, prophecy, questers, good and neutral lycanthropes
Church of Shar (G) NE
Cavern, Darkness, Evil, Knowledge
Dark, night, loss, forgetfulness, unrevealed secrets, caverns, dungeons, the Shadow Weave, Underdark
Church of Sharess (D) CG
Chaos, Charm, Good, Travel, Trickery
Hedonism, sensual fulfillmant, festhalls, cats
Church of Shaundakul (L) CN
Air, Chaos, Portal, Protection, Trade, Travel Travel, exploration, caravans, portals
Church of Shialla (D) NG
Animal, Good, Plant, Renewal
Woodland glades, woodland fertility, the High Forest, Neverwinter Wood
Church of Siamorphe (D) LN
Knowledge, Law, Nobility, Planning Nobles, rightful rule of nobility, human royalty
Church of Silvanus (G) N
Animal, Plant, Protection, Renewal, Water
Wild nature, druids
Church of Sune (G) CG
Chaos, Charm, Good, Protection
Beauty, love, passion
Church of Talona (L) CE
Chaos, Destruction, Evil, Suffering
Disease, poison
Church of Talos (G) CE
Chaos, Destruction, Evil, Fire, Storm Storms, destruction, rebellion, conflagrations, earthquakes, vortices
Church of Tempus (G) CN
Chaos, Protection, Strength, War
War, battle, warriors
Church of Tiamat (L) LE
Evil, Law, Scalykind, Tyranny
Evil dragons, evil greed, reptiles, Chessenta
Church of Torm (L) LG
Good, Healing, Law, Protection,
Strength
Duty, loyalty, obedience, paladins
Church of Tymora (I) CG
Chaos, Good, Luck, Protection, Travel
Good fortune, skill, adventurers
Once part of Tyche
Church of Tyr (G) LG
Good, Knowledge, Law, Retribution, War
Justice
Church of Ubtao (G) N
Planning, Plant, Protection, Scalykind
Creation, jungles, Chult, the Chultans, dinosaurs
Church of Ulutiu (D) LN
Animal, Law, Ocean, Protection, Strength
Glaciers, polar environment, arctic dwellers
Church of Umberlee (I) CE
Chaos, Destruction, Evil, Ocean, Storm, Water
Oceans, currents, sea winds, waves
Church of Uthgar (D) CN
Animal, Chaos, Retribution, Strength, War
The Uthgardt barbarian tribes, physical strength
Church of Valkur (D) CG
Air, Chaos, Good, Ocean, Protection
Sailors, ships, favorable winds, naval combat
Church of Velsharoon (D) NE
Death, Evil, Magic, Undeath
Necromancy, necromancers, evil liches, undeath
Church of Waukeen (L) N
Knowledge, Protection, Trade, Travel
Trade, travel, wealth