I plan on the final boss battle in my campaign to be against a god. For context, the villain has spent the campaign preparing to cast the spell Karsus's Avatar and replace Mystra as the god of magic. I want the players to enter the room mere rounds before the spell is complete. There will be a large number of one hit enemies protecting the BBEG while the spell is being finished. 

One the ideas that I have for the mechanics so far is having a number of large Chardalyn crystals that contain a portion of the divine energy, the players will break these and ¨overload¨ the BBEG, for lack of a better word. This will be how they manage to kill him. I also don't want to have a stat block for the villain as to make him feel more like a god and less like just another monster. He will be weakened due to having an influx of new power he doesn't know how to wield, but he will still be extremely powerful.

I was looking for some help on how to run this encounter?

Edit: To clarify on some terms:

           Karsus's Avatar - This was a 12th level spell from the times of ancient netheril that let the caster take the divinity of a deity of their choosing.

           Chardalyn crystals - These were black crystals mainly found in the plains of standing stones in the anarouch desert, they can be used to store magical energy to cast spells(Kinda like the ring of spell storing except you need to break these to cast the spell). It doesn't directly state that it can do what I wrote it to, but I can change them for the sake of the campaign.

mayeb put some protections around the crystals? from your writing it sounds like the crystals are just laying around

Yes, they weren't just going to be laying around. I planned on there being four crystals that are the size of a large creature. They would be pretty tanky and not just a one hit kill, I'll write in some magical shielding or something along those lines. Another thing I was thinking of adding was a random magic effect when they were destroyed, like the wild magic table but more dangerous and powerful.

well maybe OHHHH! inspiration! maybe the crystals have the statistics of a proper and can move around? or maybe I'm just spitting frogs

Sorry, I'm a bit confused about what you mean by the ¨the statistics of a proper", is that some sort of construct, I can't seem to find any stats. 

oh. sorry typo. I meant roper

Oh, no problem, though I don't know if that is what I want. It may be cool to have some sort of damage dealt to people too close to them though, kinda like they are randomly lashing out with magical energy or something.. 

I don't think I'd make the crystals "Creatures" as that feels like the wrong vibe. I'd probably go with different inanimate obstacles around them, such as a moat/chasm or a wall of fire. (Ideally more unique, I'm just pointing direction.)

You might also want to have some minions be assigned to specific crystals, to prevent them all being drawn away.

The fact that the crystals can be broken from range is a big problem. You could have a magic distortion effect messing up shots, (although then it's going to be hard for archers/spellcaster PCs to smash crystals at all).

I'd suggest that the big boss should be able to spare some concentration to fight in the battle a little. It feels a big weak for him not to be involved, and It can showcase how powerful he already is ("Look what he's doing despite the majority of his concentration being elsewhere")

If you don't want to have a stat block for the BBEG, then you could consider running it as less of a combat encounter and more of a high stakes skill encounter, or Complex Trap. There'd still be initiative and a main goal, but the "attacks" will be a lot more freeform and the risk may be more on a apocalypse/ catastrophe scale than simply a tpk. Maybe if this new god comes to power, their first task is destroying a nearby city or something, and with every round the get closer to that goal. 

I'm personally planning on running my own end-of-campaign BBEG encounter this way, as a hybrid between combat and skill challenges. 

Those both sound great. I was planning on the crystals being relatively easy to reach due to the BBEG not anticipating the players reaching this far, the challenge would be distracting the boss enough to take them out. I did have an idea of having a list of attacks/actions prepared that the boss would go through during the fight. II would also make attacks against him not do meaningful damage but maybe make his next attacks weaker. 

If you can, check out the last mini adventure from Lairs of Etharis, it sounds a lot like this. There are 4 pillars the players must destroy, but each one is attuned to a different element and protected by a powerful creature (a troll of some kind I think iirc). There's some mechanics around it too so that they can't just walk up and wallop the pillar or whatever. Worth a look I'd think for more inspiration.

Oh, great idea, maybe the first stage of the battle is after the boss completes the ritual and doesn't focuses on the players, but then the players destroy the crystals and then weakens the boss enough to take on a straight fight.