I had an idea that I am struggling to get the final pieces together, more on trying to figure out good minions and how the Big Bad dude could be handled in the final fight. I'll try to summarize it as completely and shortly below.

A town that is being raided weekly by a herd of Undead Centaurs (borrowing Matt Mercer's idea from the Tal'Dorei book) and are led by a Huntsman (Champion Stat Block) riding a Nightmare. The players can fight/investigate this to find like an underground compound, complete with zombies, Minotaur Skeleton, more Undead Centaurs, and even a sort of Sarlacc pit that is consuming bones/corpses. The BBG behind this is the tavern owner of the aforementioned town, who has been sending adventures to their doom. He is a Necromancer, looking for a different path to Immortality besides Lichdom, trying to figure out how to turn himself into a true Vampire. He has also charmed an old gnome wizard that the players have interacted with before in an earlier town, who strangely disappeared without notice (they didn't investigate, as it was written off as him searching for magical treasures). The Huntsman would either be a mid-boss fight before the BBG, or part of the BBG fight as a 'front line' defense. 

Basically, I'm stuck on how to set up the BBG encounter. I have him written as a slightly changed Necromancer from VGM, but if he does change to a Vampire, the Vampire stats in the MM seem kinda OP to just add to his base. Also, just not very familiar with how Vampires work in D&D, as far as killing them for good & how the Charm might be broken (if that can apply to the NPC the characters already knew). 

Any feedback on this type of adventure would be great, also anything on understanding how the mechanics behind the BBG encounter can work to make it a pretty difficult fight. 

What level are your players and how many of them are there?

4 Players now, just hit lvl 6. Still the Eldrich Knight, War Cleric, Draconic Sorcerer, and Open Palm Monk from one of my last threads (I can't remember which one I said that stuff on). 

You could use the stats for a vampire spawn and claim that while whatever procedure your villain underwent was successful, but caused him to start off their new unlife as a fledgling vampire.  Assuming he is intended to be a boss during this leg of your campaign, with a CR of 5, he'll be sturdy, but not unbeatable.  And with a vampire spawn's claws hitting for 2d4 + 3, it's not all that different from a sword's damage.

This is a really cool idea. I'm still a little worried about having that CR rating be the boss. I threw a Young Green Dragon at them at level 5 and they were roughly just over half health going in, and they took care of it pretty handily. 

I had thought of using Vampire Spawn in the dungeon crawl, then like leave information in the loot hinting to that all the vampire spawn were previous adventurers the BBG has been experimenting on, causing them to become Spawn rather than full Vamps. 

Maybe I just need to fight like 'more efficiently' with the BBG and minions, that may be a coming with time thing sadly. 

If they thoroughly thumped a green dragon (even a young one) while at half HP at level 5, then maybe an encounter with a full fledged vampire as a boss isn't too far a stretch.

As for breaking the charm on your NPC, I imagine you can RP an exorcism of some kind with the war cleric to break it.  It doesn't need to be anything fancy, since the charm effect itself is most likely going to be undetected until something happens that really underlines that things are not okay with the NPC.  Recognizing that the charm effect exists is the big challenge, removing it, though, if you look into vampire lore, is usually as simple as having the influenced individual hold or look at a holy icon of some sort.

I think that's what I'll end up doing. Some sort of 1st-round transformation for the BBG, going from Necromancer to full Vamp. I like the idea of the charm continuing to after the encounter, good shout there.

Any idea of other kinds of minions/mini bosses along the way or part of the final battle? Atm, I'm just kinda mixing other undead things and then a few Vamp Spawn to represent the experimented on previous adventurers, then the Champion+Nightmare as another fight (basically having him be a RP of a man driven to extreme measures trying to bring back his wife/daughter, and the Necromancer promised he could). Any other ideas of creatures I may be missing is appreciated, as has been your help so far :)

The creatures you mentioned should be sufficient.  Throw in the vampire's charm ability on one of the PC's for good measure, and the fight should get pretty dramatic fairly quickly.