That's... a lot of questions. I'll answer the ones I can

* SR weapons - useful if you don't have enough SSRs for a full grid, or if you have a Phantom weapon in your grid and you *need* 6 of one type of weapon, and don't have enough SSRs to field. But mostly they make good fodder for skill level ranking. Give each one 6 R grade weapons (but not enhancement material R grade, which has zero Skill Level raising potential) and it gives 140 skill points.

* 100% Eidolons are actually 80% Eidolons, plus a bonus based on number of Eidolons that match that element.

* Yes, it's % which each weapon gives. I wouldn't bother with the formula unless you're trying to decide between two different bonuses. So, say you have 200 Assault Weapon and 100 Eidolon Attack up, but zero Eidolon elemental bonus. Because you are 300% up already, a bonus of 10% Elemental bonus will be worth 40% Attack bonus. So picking a Kamihime who gives, say, +10% elemental over one that gives +20% attack would give you more damage.

* Soul selection - everybody has an opinion, most are different. Bear in mind - first top-grade soul is quick to get, then it becomes a grind to get to the second. The choice should be based on who will help you farm the most. Most people will tell you not to do Andro, because if you aren't doing enough damage in a battle, more healing isn't likely to save you. I tend to find I want more Andro-users in my raid battles. Herc is a good choice, and D'art is useful at least because Sniper Shot will feature as your bonus ability when running Shingen (the ultimate objective until T4 souls are released). I think the smart answer is, whatever your best team is shortest of. If you have no healers, then I'd stick with Andro personally. If you have 1 good or 2 mediocre healers, then shoot straight for Herc or maybe even Solomon for Tower farming.

<reads rest of detail of team>

Sounds like you have healing covered, so possibly Joan is the better choice.