I remember a discussion long ago in the 3e days about which Mulhorandi deity would be most likely to survive if they and the Faerunian deities were forced to compete due to their geographical regions merging (which was hinted in various 3e books as possibly being in the cards, before the Spellplague thoroughly wrecked everything of course). It was pretty much agreed that Isis would be the most likely to survive, since the whole "motherhood/childbirth/home and hearth" portfolios were still relatively open; while Chauntea and (to a lesser extent) Lathander have a sort of vague overview of those portfolios, they aren't their main focuses. So bringing in a newly-returned Isis who is attempting to become the deity of motherhood and home would actually be a decent idea...
I want to make sure the story with Isis ties back into SKT. Given she is concerned with home and hearth then the hill giant raids on the farms in the north will affect this aspect. In addition, Isis is linked to storms, but I feel she is not as strongly linked as the other deities of storm. My current thought is that she will be aware of the trouble the storm giants are facing, but not know the specifics. The net result should give good reason for Isis to involve one of the PCs that is also linked to water and growth. Isis can also show up in the PotA story near the water node or be tied in with events that occur in the Golden Fields.
The deity Geb will also be involved. This deity will have survived the spell plague with the aid of Isis. His story can intersect with SKT and the PotA story. The link with PotA will be through the fire node, although I'm not sure of the specifics. The current plan is to have him ask the barbarian that is strongly tied to fire and has a minor link to Maegera to set up a new forge in the fire elemental node. Then be asked to gain alliances with the Dwarves by returning the portion of Maegera that was stolen by the Drow and given to the Fire Giants.
The net result, with player cooperation, should be a couple PCs that are leaders in the faith for Isis and Geb. I'll get a chance to use more than two of the dungeons in SKT with good reason. Character development for these two characters should be interesting.
Additionally there will be an interaction with Auril and a warlock character. Auril will want the Frost Giants to find the Ring of Winter. This will give the warlock player some interesting conflict to resolve for his character. I may end up looking up opinions what happens when a warlock no longer has a pact with a patron. Alternatively, I think the player wants to switch to a Hexblade, so this question may become moot.
The last character, a paladin, will most likely become a paladin of Bahamut. This will interact well with both the Fire Giants and the reason for the Ordening being messed up. The character may be put into a bit of conflict in that they may find a need to help the giants who hate dragons.
Thank for the feedback and guidance on finding a reason for deities to spring up in the FR.