I have already converted all of the encounters from part 1 of the adventure. I got stuck when I started converting the NPCs in the towns and cities, some of whom are clerics. There are also clerics on the enemy side - the very first encounter of the adventure includes one, but at least the enemy clerics all follow Tiamat. I didn't want to include Pelor, Wee Jas, Erythnul, etc, but haven't been able to figure out who to replace them with. I also need to decide if I even want clerics or not.
I've also had the idea of replacing the goblinoids. If I place the adventure in the Eldeen Reaches of Eberron, I'd replace them with fiends and human barbarians from the Demon Wastes. If I stick with homebrew, I may make them Cult of the Dragon followers (using the stats from the Tyranny of Dragons campaign) plus draconians and abishai in place of the dragonspawn. Partly to mix things up a bit more.
When I recently started a Greyhawk campaign (actually 2: one in 2e, and one with Beyond the Wall, in two separate areas of Oerth), I wanted to basically do the same: rein in the hundreds of Greyhawk deities and have a tightened Pantheon. Once I started into it, I found it was a lot of work to narrow things down, keep them balanced against each other, cover all the spheres, etc. I eventually gave up, and decided to focus on the area I was in (as mentioned before), and so I basically have: Rao and Cuthbert in Veluna, and Heironeous in Furyondy. Iuz is Iuz in his lands, and there was mention of Nerull to the east. That's it. Now, there may be more, but I'm going to focus my NPCs around these while the campaign runs here. I've found tons of options online around alt Pantheons, alt names for deities, etc. They're all in my "ideas for future games" folder.
Ditto on replacing Humanoids. Problem was I couldn't find any established humanoids along the lines of Orcs, Goblins, Hobgoblins. For my Beyond the Wall, I'm starting with Goblins, but using an old Greyhawk name for them: Jebli. I also have them referred to as Wisplings in the area of Sterich where the characters are starting. So I basically reskinned and renamed the Humanoids - the players don't know the difference - and then I can just have larger and stronger versions with slighly different names. I also added Harrow Hounds, that travel with the Jebli (goblins) as trackers and hunters. They're just dogs or wolves, or Dire Wolves as necessary, but again, the players don't know that. BTW also has rules for different types of Goblins - Mountain, Steppe, Deep, etc. where they have bonuses in their home environment and get weaker the farther they go from it. I've already used it to have Mountain Jebli down on the plains, and they were weak(er) when encountered. Now the party is going to the mountains to find out why they travelled so far afield.
Unfortunately, while I love dragons, draconians, and such, I fell like everything that is put out recently, from WOTC, and AL is all focused on Dragon Cultists and Dragons. Its sort of jumped the shark in our group. Using demons/devils, draconic lower planars, and cultists may work, but it seems overdone (again, in our experience).
I like your fiends and human barbarians from the Demon Wastes idea. Give them some corrupted ogres, abishai, etc., and pick a deity for them to be following (or demon prince) for their clerics, and off you go.