Shadowdale
Event - Fall of the Gods
The characters are relaxing at the Inn in Katina when the events described occur (not Arabel).
Consider making the Midnight character be one of the party (Gal or Kat or an NPC?)
When the event occurs, the ship of 509 will be journeying. The scrying devices (when they work) will reveal that Phantoozie will not come to Kopeta until the magic situation changes. He doesn't dare risk bringing the ship down "what with the magic gone wonky and all".
Caitlen Moonsong will arrive at the Inn saying she was sent a magical message from her "patron" pleading for quick help. This is the first village she has come to since receiving it. She will be totally evasive about why she was in the area saying "it is private business of my own and has nothing to do with the current situation. Ask me again later and I may tell you."
It will probably be best to not have Beourn or Ulla participate in this adventure. It should be easy to keep them busy recovering or studying for the next body part. Depending on how the adventure ends, it may be advisable to include the two of them in the ending to let the party know for certain that all the changes, deaths and disruption is a result of their meddeling in the affairs of the gods!

Event by Event changes needed:

Chapter 1
Event 1 - The storm
The townspeople will be the first to alert the party to the coming storm. The farmers and early rising leaders will go to the Inn and wait for one of the party members to come down. They will wait no longer than 1.5 hours after sunrise (which is at 6:20AM). The party may try to mitigate the damage from the storm and help the folks get ready, but soon it will be impossible to move about without being blown away. They will be advised to seek shelter in a cellar or something that will keep the 509 together and allow the one chosen as Midnight to make her entrance.

Event 2 A
Allow the char chosen for Midnight to pick a spell.
Event 2B the entrance will be at anyplace the party has holed up. They may have been worried about the missing char during the wait time.

Once the storm has passed, the party will probably begin to repair the damage. This is when they discover the unreliability of magic. Substitue this event for the listed Event 5. Develop rolls for determining the damage and injury from the storm on the buildings of Katina.

Event 3
The party will notice this the next morning most probably. Early that morning, Alarantha with Duckey in tow will arrive to see if they are having the same problem praying for spell that she has had.

Event 4
The crying woman will arrive several days after the storm. She received the word of the absence of Lovitar sent to all in the temple in the form of a talking bat. The news has left her almost broken. She will either arrive at the Inn or be found on a trail by someone and brought there.

Event 5
Skip this as the party will found out about it as soon as they are trying to clean up the mess left of the storm.

Event 6
This is a problem. It is too unlikely that a character like this (Ulgon) would wander into the Inn. Best guess is that this will be an encounter while on the road to Castle Killgrave in Northern Comyr.

Encounters
Encounter 1 - Request to keep the peace from city guard. This is changed to be the new commander of the Waterdeep outpost near Katina.
Encounter 2 - This harpest character encounter can occur in the Inn during the time after the storm and before they leave for Killgrave.
Encounter 3 - Harassing Priests of Bane. Could this be moved to occur just after the party enters Cormyr territory?
Encounter 4 - Terrified Cleric of Torm. This might be placed in the wilderness. The cleric is a cloistered cleric observing a year of hermit isolation. The party are the first persons he has seen since the storm. Should probably happen soon after the party leaves Katina.
Encounter 5 - Helpful Guide. Don't use as its not needed.
Encounter 6 - Prophetic Madman. Any ol'e time!

Mini adventurers
1 - Bad crystal balls, Don't use
2 - Peryton, don't use
3 - Sacred Snake - could happen on the way to Killgrave
4 - Dancing Dopplegangers, don't use
5 - Haunted Teahouse
6 - Beautiful Lycanthrope - This could be a new person from Waterdeep arriving in Katina to build her mansion. Review this once all the modules are available.

Arabel Rumors
The party will stop in some city before getting to Killgrave (probably Arabel). Use these rumors at that time, adjusting them for the current conditions.

Chapter 2
Event 1 - This event will occur directly after event 5 of Chap. 1. Caitlin will be taken to a room where her wounds will be discovered.
Event 2 - The party will be unable to cure her, but MUST go on with the adventure.

Once on the road, the items defered from Chap. 1 will occur. These are/may be:
Encounter 4 and Mini 3
As there is far more disturbances, all encounter checks occur at a -1 (a 1 or less indicating an encounter)
They arrive in Arabel
During their stay to relax and replenish their stores before going on to Killgrave, they may find Mini 5.
Trot out the rumors at this time.

Event 3 - Undead Ambush Once they are back on the road, shoot them this encounter. Pick a more powerful undead though, maybe the special BaneGuard.

Event 4 - As described; no changes.
Event 5 - On the journey out of Arabel. As described.

Encounters
Encounter 1 - OK as is.
Encounter 2 - OK as is. Note that Stallen will be able to tell this is a Harper and will get not only the information detailed in the description of this encounter, but also any true rumor from Arabel the party didn't find out. He may also tell them of the false rumors they heard as "nothing more than fear talking."
Encounter 3 - Veltar. Veltar is a 9th level mage with 30HP and a large spell list heavy on misdirection, escape and stealth spells.
Encounter 4 - OK as is.
Encounter 5 - OK as is.
Encounter 6 - This will have to be heavily modified if the bandits are to pose a serious threat to the party. It should probably not be used. Think about creating a more dangerous encounter for the party here.

They arrive at Killgrave

Chapter 3
Instead of a catapiller, use a fiery ball of energy to split the party initially.
The noises will be hear from every direction and may chars will hear distintive sounds of their worst foes.
Remember, it is the will of Bane that is splitting them up; very little will allow them to form even groups of two!
Determine in advance what the "fondest desire" of each character. Some I know now are:
Timber is invited by an ancient dying Driud to watch over a sacred wood that has not been disturbed for 390 years. He is told that he will be raised in levels by the death of the other Druid.
Victorex will be offered the money and power to create a true temple of Bob in Waterdeep by the Grand Priest of Bob.
Krom will find a dungeon room with a demon and behind it a pedistal with a ring on it. The carving on the pillar reads "The one who slays this beast will become a Demi-God when this ring is worn".
and so on.

The body of the goddess is guarded by 20 Bane Guard who can not be turned (as their creator Bane is controling them). Also, there are 2 of the Hakeshar and 5 birds (one of which is Bane).

The rest is as written.

Chapter 4
Encounter 1 - The wise Druid. He was attracted to the explosion which he heard more than 5 miles away. He took bat form to get here and will be friendly to the party if they do not menace him.
Encounter 2 - Thug Attack. The objective will be to isolate and capture one of the party for interrigation. They will flee in different directions once this has been accomplished and take the captive to their nearby cave/lair. If a battle occurs, the men have been instructed to flee after 2 rounds of failure to capture the one they chose.
Encounter 3 Strange Wind. As written, but more mysterious. Make it obvious that this strange wind is coming from gates, portals or other supernormal sources. It is an ill wind indeed!
Encounter 4 - Magic Mouth. OK as is.
Encounter 5 - Cult of the Dragon. This dragon is twice as old as detailed. It should represent a dire threat to the party and they are glad when it is driven away.
Encounter 6 - This character needs to be at least 4th level to keep up with the rest. Modify char sheet to reflect this.

Chapter 5
Event 1 - The Helpful Paladin. As written. Really play up the staunch lawfulness of the Paladin
Event 2 - Woman on Pegasis. Although the Harper flies on, she encourages the party to meet the Wraiths to "delay them and reduce their numbers at least!".
Event 3 - Traveling again. Lots of wilderness encounters, but not many with normal animals.
Event 4 - A Doggy Kidnap Attempt. There are 12 dogs, 8 level 6 thugs and 4 clerics that are 8th level.
Event 5 - Forest Sage. OK as written.
Event 6 - 20 Bane Guard are risen; one from each major bone of the hand and fingers.

Encounter 1 - OK as is.
Encounter 2 - Tilverton. OK as is.
Encounter 3 - Another Floating Skull.. OK as is.
Encounter 4 - Help on the Hoof. OK as is. Perhaps make this following initial Harpy attack.
Encounter 5 - Swooping Harpies. 1/2 of the sister Harpies will attack and the other half follow them as mess with them.

Chapter 6
Event 1 - OK as is.
Event 2 - Elminster. He will talk of more than just the current crisis. If they will stay to help guard the temple Lathander he will tell them something usefull of their larger quest.
Event 3 - Old Skull Inn. The party will encounter other folks from their last visit. The harper woman Silverheels? will inquire after Stallen for instance.