How I run Clerics and so forth.

More LotFP houserules. 

Alignment

Here's how I handle alignment. 

Lawful refers to the divine plan for the cosmos. It is associated with things that are holy (such as nuns/monks, relics, holy sites, and so on), with destiny, and with spiritual enlightenment. The divine is beyond human understanding. The western church's worship of 'God' is a manifestation of this, as are various eastern spiritual traditions. 

Chaotic refers to things that are outright against the divine plan. Magic draws on things outside of our universe and is directly in opposition to the natural divine harmony. Chaotic things are magical, unnatural and alien. 

Neutral refers to the mundane world. It is, essentially, broken. Impure and flawed, since it is no longer proceeding according to the divine plan. It is not, however, actively against the plan in the same way as chaotic things are.

All clerics must be lawful, since their abilities are directly powered by the divine. All magic users and elves must be chaotic, as the magic they use is fundamentally against the divine plan. If a cleric stops being lawful, or a magic user or elf stops being chaotic, then they lose all their spells and any other supernatural abilities.

Most other characters are neutral, but they don't have to be. A chaotic character might have a bloodline tainted by magic, or a lawful character might have been touched by a saint and brought back in line with the divine plan. 

Particularly powerful contact with magic or the divine might make a neutral character become lawful or chaotic.

Clerics

Clerics are mostly religious figures from their local communities. I'm assuming a game run in essentially late-medieval Britain here, so the majority will be Christian priests, monks, nuns or similar. In a different setting, clerics would come from different walks of life - Roman haruspices and pontifices, or Indian yogis and fakirs come to mind.  

Clerics prepare their spells like in the core book, at a set time each day; generally at dawn, midday, dusk or midnight. To prepare spells, you need to consecrate an area first, with at least the following:

• The consecrated space must be clearly delineated.
• All chaotic or otherwise magical things must be removed from the area. 
• A symbol of the cleric's faith must be present. 
• A turn must be spent cleaning and ordering the space.

If this is done, the process of preparing spells takes hours if the most valuable holy symbol you've got is wooden (or of a similar value), turns if the most valuable holy symbol you've got is steel (or similar) and minutes if the most valuable holy symbol you've got is silver (or similar). You can only prepare each spell once - you can't have two slots hold the same spell.

If you had prepared a spell for the day, and used it, you can re-fill that slot with another spell of that level you haven't yet prepared. You still can't prepare the same spell twice in a day. If you missed your allotted time to prepare spells, you've got to wait until the next day.

To do this, again you need to consecrate a space and pray/meditate for the spell. This takes as many minutes/turns/hours as the spell's rank. Once this is done, make a save against magic; if successful the spell is prepared. If failed, the spell is lost and you can't prepare it again that day. You can improve the power of your consecration with all the following:

• For each silver piece of food or wine you offer as a sacrifice during your consecration, improve your save by 1.
• For each lawful supplicant who takes part in the ceremony, improve your save by 1. Neutral supplicants can also join you, but only actually help if they succeed on a charm skill roll. Chaotic supplicants aren't welcome.
• For each supplicant who takes 1 damage offering blood as a sacrifice, improve your save by 1.  

Clerical Scrolls, Holy Water Etc.

Things like creating scrolls of clerical spells, holy water, and so on all work exactly like in the core book. They can't, however, research new clerical spells. Any cleric can automatically read and use any clerical scrolls (and similar items) that they find.  Any lawful or neutral character can identify and translate the scroll with a successful appraise roll. A lawful character who can't cast spells can still use a clerical scroll (or similar) if they can read it and make a successful save versus magic. If the roll is failed, then the spell fails and the power is used up.

Cults

The religion a character follows defines which spells they can access. The default cleric spell list in the core book is for Christian faiths; members of other cults will use altered spell lists, which may include custom spells just for that cult or spells from the magic-user list. I'm not sure if Jewish clerics would use the same spell list (since it's essentially biblical in flavour) or have a slightly different one. When a player wants to play a Rabbi, I'll work it out.

You can't use spells from outside your own spell list, including casting them from scrolls or similar. You can, however, convert to a new faith. This probably takes a few months, but other than the role-playing and loss of access to some spells, there's no penalties for it.

An Example Cult - The Sol Invictus

The cult of Mithras, the Sol Invictus, worship the sun as a manifestation of the divine. They were a mystery cult at the time of the Roman empire, and persist to the modern day, in an underground, secretive form. The cult's mythology contrasts darkness and light, with symbolism of secrets and mysteries being uncovered by the light of enlightenment, and this is reflected in their spells.

Rank 1 - Bless, Command, Cure Light Wounds, Detect Evil, Identify, Light, Protection from Evil, Sanctury, Turn Undead

Rank 2 - Augury, Continual Light, Enthral, Forget, Heat Metal, Heroism, Resist Cold, Resist Fire

Rank 3 - Cure Disease, Detect Illusion, Dispel Magic, Magic Vestment, Remove Curse, Sacrifice

Rank 4 - Cure Serious Wounds, Detect Lie, Divination, Protection from Evil 15' Radius, Spell Immunity, Wall of Fire

Rank 5 - Commune, Cure Critical Wounds, Dispel Evil, Quest, Secret Chest, True Seeing

Rank 6 - Anti-magic Shell, Forbiddence, Find the Path, Heal, Tongues, Word of Recall

Rank 7 - Holy Word, Earthquake, Remote Surveillance, Vision