So like, some ability says "You gain skill focus, but must choose X, Y, or Z"? If the skill focus feat is bootstrapped, then you can set the candidate expression field (usrCandid1) directly in the bootstrap. If it is added to a table by a user, then you'll need to transition to the correct copy of skill focus and set that field in a script.
As for setting the class skill, you'll need to get to the correct copy of the feat. If bootstrapped, define a Custom tag to serve as a marker and assign it as part of the bootstrap. If added to a table, there should be a combination of tags you can use within a findchild to get you there (I believe most tables have a tag which means "taken within this table" and you can combine that with the thingid tag of the feat to get to the right copy).
Once there, check to confirm the feat has made a selection, and if so, transition through the "chosen" link to get to the correct skill and assign Helper.Proficient. Tell me if I am on the right track and give it a shot yourself. If you need further tips post what you're trying and I'll try to aid further.
