Lets go through a few things

• Clerics pray and prepare spells once per day, this determines all their spells for that day
• Clerics get additional spells to prepare depending on their wisdom bonus. These spells (as well as their base spell allowance) are alignment restricted:

Chaotic, Evil, Good, and Lawful Spells: A cleric can't cast spells of an alignment opposed to her own or her deity's (if she has one). Spells associated with particular alignments are indicated by the chaotic, evil, good, and lawful descriptors in their spell descriptions.

• Clerics get one domain spell for each spell level they can cast (1st, 2nd, 3rd etc). Clerics have two domains and this bonus spell must be one of the spells from their domains for that level.
• Orisons can be used as often as you want during that day
• Spells Level 1+ are "used up" when cast, the cleric can't use them again until they've prayed again the next day
• Clerics can also Spontaneously convert any of their spells (but not their bonus domain spell) into a cure or inflict spell of the same level.

So, the Level 1 Cleric with 1 bonus spell per day from wisdom.

Gets 3 Orisons - These can be cast as often as they like.
Gets 2 level 1 spells from any of the level 1 cleric spells. These can be spontaneously converted. Once cast, these are used up for the day.
Gets 1 level 1 spell from their domain spells. Once cast this is used up for the day.

Example:

Bob the Cleric of Chaos and Charm

Bob has prepared the following Spells:
0: Light, Mending, Bleed
1: Protection From Law (Bob is allowed either Charm Person or Protection from Law from his domains)
1: Bless
1: Doom

Bob can cast Light, Mending and Bleed as much as he wants.
Bob can cast Protection from Law, Bless and Doom once each per Day.
Bob could, if he wanted to, take 2 "Doom" spells as his non-domain spells instead, and as a result could cast Doom twice per day - what he chooses for his spells is entirely up to him.

Don't forget also the clerics highly useful channel energy ability!

Yes

Once I choose... inquisitor spells am I able to swap out any of these spells with different spells from the list of Inquisitor spells? Yes, on a limited basis, starting at level 5.

Upon reaching 5th level, and at every third inquisitor level thereafter (8th, 11th, and so on), an inquisitor can choose to learn a new spell in place of one she already knows. In effect, the inquisitor "loses" the old spell in exchange for the new one. The new spell's level must be the same as that of the spell being exchanged, and it must be at least one level lower than the highest-level inquisitor spell she can cast. The inquisitor may swap out only a single spell at any given level and must choose whether or not to swap the spell at the same time that she gains new spells known for the level.

It's easy to miss, buried in a wall of text.