Generally you want to plan out encounters with the CR based off of your Average Party Level (APL).
The Core Rulebook provides the following guidelines:
APL -1 : Easy
APL +0 : Average
APL +1 : Challenging
APL +2 : Hard
APL +3 : Epic
The encounter you propose would be APL +4, so harder than epic on paper, however, when you have the PC's gang up 4 v. 1, CR becomes a lot less relevant. Single enemy encounters tend to be less challenging than those with multiple targets simply because of the action economy in combat. The party is going to be able to do 4x as much in a round, typically.
You could handle it like this
1x Wizard 7 (CR 6) 2400 xp
-AND-
2x Fighter 5 (CR 4) 1200 xp each
-OR-
4x fighter 3 (CR 2) 600 xp each
-OR-
12x Fighter 1 (CR 1/2) 200 xp each
Mix and match lower level minions until you come up with 4800 xp total for the encounter, making it a CR 8 encounter, and thus at the top of what the PC's can reasonably deal with. Have the fight take place in a long, narrow room, so the mooks can spread out in front of the caster (who should be flying, anyway), while they run interference the caster pelts the party with spells. It may also help to throw a cleric or two in on the bad guys side. A bard in an encounter like this can act as a great force multiplier, as well, letting the enemies hit more often and for more damage. If I was writing it up, I'd probably go:
Wizard 7
Bard 3
Cleric 3
6x Fighter 1
Before combat (if they have a chance) the wizard casts False Life, Mage Armor, Shield, Levitate (Fly if he knows the party has the ability to fly) and Haste.
On the first round of combat the bard begins performing, the cleric holds his action to heal, the wizard moves up and fireballs the party as the come in the door, and the fighters move up to threaten the entire width of the room (they should be using polearms of some kind, glaive-guisarmes work well, since they can then brace for a charge). Once the party hits the spear wall, it will devolve into a free for all and you should adjust tactics accordingly, but that opener will really drive home the "boss fight" feel you want for this without going with the mechanically weaker single boss battle, which is tough to do for NPC's (not nearly as hard for a monstrous boss like a dragon or something).
Anyway hope that helps.
EDIT: Just remembered the Bard isn't in the BB, nor is the Glaive-Guisarme likely to be.
You could still go with this, in which case check out D20PFSRD for the full rules for Pathfinder.
Alternatively you could stick with the BB content, run with 2 clerics, and swap the weapons out for something with reach (and brace, preferably, but I can't remember if that quality was included in the BB). I would recommend sticking with the content you're familiar with, though 5th level would definitely be a decent place to begin transitioning to the full rules if that's your plan.
I don't like the APL system they use to make an adventure, Obviously a party of 5 people with an APL of 3 will be more powerful than a 2 player party with an APL of 3. Despite sharing the same APL.
Yes, but the baseline assumption is a party of 4. The APL section specifically mentions that it has to be adjusted for parties of more or less. Less than 4 is typically much more difficult to adjust for and it's easier to use NPC's to balance things out. More than 4 is much easier to adjust for. 4-5 typically the adventure can be run as written, 6-7 adjust the encounters up by 1 CR, 8-9 adjust by 2 CR, etc... APL works a little better if, instead of averaging, you add the party level together and divide by 4 regardless of party size. Thus a 5th level, 6 person party has an APL of 7.5, rounded down to seven, but that .5 is important to keep in mind, since it means that their upper limit is just a little bit higher than a typical APL 7 party.
It works a lot better if you remember that it's just guidelines, and is built to certain baseline assumptions that every game may not conform to. There's a bit of a learning curve on what's overkill in these situations and what isn't, and my typical rule of thumb for it is to err on the side of underpowered when you're unsure. Sure, it may not make the encounter as challenging and dramatic as you want, but there's always the next BBEG to write up.
Another thing to bear in mind is that, while you may see flaws in the APL for different groups than the one that you're running for, you are running for a 4-person party. The APL system was designed specifically for it. This is an ideal opportunity to get used to using it, since you will be able to see the flaws and wholes in it now, and be more comfortable working around those in the future when you may be forced to plan for a larger sized party.
A good challenge for 4 level 5 characters is a level 8~ NPC (CR 7) with two level 4 mooks. (CR 6) CR7+CR6 = CR 8 which is Epic.
If you put one guy versus 4 people, it's really likely that the one person will just get swarmed-- then, too much depends on uncontrollable variables and it's likely he'll just go down. But with two mooks with chunks of HP who can do credible damage (like, a minotaur), the party has to micromanage their combat strategy more effectively, crippling one enemy while controlling the others. If they let them all just go ramshod on them, they'll be overwhelmed.
I don't like the APL system they use to make an adventure, Obviously a party of 5 people with an APL of 3 will be more powerful than a 2 player party with an APL of 3. Despite sharing the same APL.
5 people with APL of 3 is pretty close to 5 level 2 characters played by veteran gamers.
2 people with an APL of 3 is pretty close to 2 level 5 characters played by newbie gamers.
It's like the pirate code. It's more like a guideline than a set of rules.