I'm trying to homebrew a Favored soul for a D&D 3.5 game and I have a couple of questions.  First, which ability score do I use? Both Cha and Wis are mentioned,  Cha for the ability to cast spells and Wis for the spell DC. Second, how can I easily link the Clerics spell list to the Favored Soul since they use the same spell list?

That's an odd set up. If CHA is the main score, it should dictate DC, but you can change the DC for the class using the BONUS tag. Just realize you need to use Score IIRC.

The biggest issue that I'm having at the moment is I don't know how to link the clerics spell list to the Favored Soul Class.

On the class line you need the tag:

SPELLLIST:2|Favored Soul|Cleric

From the documentation:

*** Updated 5.11.4 ***

Tag Name: SPELLLIST:x|y|y

Variables Used (x): Number (number of choices)

Variables Used (y): Text (Class Name)

Variables Used (y): DOMAIN.Text (Domain Name)

What it does:

• This is an optional tag with PCGen defaulting to the class name as the name of the spell list if this tag is not included.
• Following the number of choices (x), this is a pipe-delimited (|) list of class names (y) that the class can choose from to duplicate spell casting ability.
• For a spellcasting class with subclasses that have separate spell lists, the SPELLLIST tag should be included in the subclass line only.

Example:

CLASS:Faemancer <tab> SPELLLIST:1|Ranger

The class uses the ranger spell list.

SUBCLASS:Egoist <tab> SPELLLIST:1|Ranger|Druid

The subclass uses either the ranger or druid spell list.

CLASS:War Mind <tab> SPELLLIST:2|Ranger|Druid|Barabarian

The class uses 2 of the ranger, Druid or Barbarian spell lists.

CLASS:Blood Witch <tab> SPELLLIST:1|DOMAIN.Animal

The class uses the Animal Domain spell list.

CLASS:Rogue.COPY=Blood Witch <tab> SPELLLIST:1|DOMAIN.Animal

Copy class Rogue to Blood Witch useing the Animal Domain spell list.

CLASS:Defender.MOD <tab> SPELLSTAT:INT <tab> BONUSSPELLSTAT:NONE <tab> SPELLTYPE:Arcane <tab> SPELLBOOK:NO <tab> BONUS:CASTERLEVEL|Defender|TL <tab> SPELLLIST:1|Channeler

Modifying the class Defender changes all of these tags to determine bonus spells and maximum casting level.

Where it is used:

Class Line, SubClass line or SubstitutionClass line.

I've tried that and I've tried copying the tag from the Cleric class in the rsrd_class.lst file and neither is working.  I'm also realizing that I haven't mentioned what version of PCGen that I'm using, which is 6.08.00RC8 if that makes a difference.

ABILITY:Cleric Class Feature|AUTOMATIC|Cleric ~ Spells (is the line I've copied)

I'm still having trouble conecting the Cleric Spell list with my Favored Soul Class.

Did this ever get resolved?