My plan for an upcoming combat involves a heavily customized creature and I'm hoping to get an estimate of the CR both of him individually and of the encounter as a whole.
The boss is a giant fast zombie wyvern with no flight, no slam, and without the standard quick strikes; instead he has the ability to slam his head into the ceiling of the low cave the fight is in, causing a rockslide for 2d6 in 20' around him (Ref 15 half), and fast healing 5. He also has 4 skeleton minions.
When the boss's hp is reduced to 2/3, and again at 1/3, he flees to another area of the cave and summons 4 more skeletons, hoping they can hold the party off long enough for his fast healing to do it's thing.
My party is only 3rd level but they're min-maxed to hell and back. We're also using the "Armor as Damage Reduction" rules, so the group is likely able to ignore most or all of the damage from the minions, making them mostly a distraction and flank-buddies for the boss. Running the numbers, an unmodified giant fast zombie wyvern and 12 (4x3) human skeletons is a CR 7 encounter. Vicious, but my group has handled similarly overwhelming odds and come out bloodied but victorious, and as a rule we like that kind of win best.
If the minions are basically a non factor, I wouldn't even calculate them into the CR. The wyvern is only about a 4, but with tactics an a heavily optimized party you have about a CR 5 at best. Unless of course you seriously modify the statistics of the big bad. Any of my optimized parties would wreck this in about 3 to 4 rounds at most. Good luck.
Hmmm... Any recommendations as to making the encounter more threatening?
Definitely give him flight again. Why'd he lose it in the first place?
Just apply the template to a wyvern, and let it go.
Not sure why you wanted the rockslide thing, maybe just for an AoE?
It's an interesting effect, to say the least.
Another tip to make bosses last longer is to max their HP. No one wants the big boss monster to die early, right?
If the 4 skeleton summons don't hold them off long enough for you, try doing 6. Then 8 if 6 doesn't work.
There comes a time when a GM must adjust encounter difficulty on the fly during a fight, whether to make it harder or easier.
This fight is going to be one of those times.
He lacks flight because the encounter area is too small for that anyway, the cave is only 30' high on average. Also because I was a little worried it would make the fight nearly impossible as the group has almost no ability to deal damage at range, except for one person with a pistol and the few ranged spells the magus has.
Yeah, the rockslide is just so he has an AoE and to make the fight a bit more cinematic. I have decided to boost the damage to 4d6 though; enough to be a threat but, thanks to DR, not overwhelming.
Here is a good read for you:
GM's Guide to Creating Challenging Encounters
If the minions are summoned from a spell, then their CR does not count as it is an ability of the monster. If they aren't summons, then you count their CR.
If you want to add some additional challenge to the fight, consider terrain and who it is advantageous to. If the party can dog-pile the big bad in a corner, that makes the whole thing easier for them. However, if there is a chasm they can be pushed off of, difficult terrain that the big bad ignores, or some sort of hazard within the fight area, (poison gas pockets that erupt randomly?) that could make it more challenging as well as interesting from a combat perspective.
Consider that a regular skeleton can be pasted by a single channel from a cleric. Reduce the number of skeletons, but increase their CR. Give them class levels, makes one a sorc or a bard to buff the rest of them and the dragon. That adds AoE damage via spells like burning hands, or color spray. Rogue skeletons can be a pain the party's backside... literally. The extra d6 of sneak attack can go a long way to making that fight more dangerous. Use max hit points for the monsters if they characters are min/maxed.
These sorts of things will add a lot of intrigue and a sense of 'epicness' to the fight. A fight on a chasm that belches poisonous vapors from a volcanic cavern below as the group is being assaulted by arrows and spells from the other side whilst fighting the wyvern on a narrow bridge is far more interesting than: A circular cave with a 30' ceiling.