Dealing with more than 4 players standard challenge rating just doesn't work. Adding more monsters should work (if there was 2 =cr guys should be as difficult as 1 =cr guy would have been for a 4 player team). But adjusting their cr just doesn't work as well.
There are a few things you need to consider when making an encounter:
1)Attack vs Armor.
If a player focuses on something (such as armor) he should be good at it. For this reason a baseline for AC needs to be set and you need to help players find a way to reach it. For example set it that the target armor for 50% hit is level +14. This means at level 1 standard armor is 15, at 5 it's 19. For each point higher he will avoid a hit 5% more often and each point lower he will get hit 5% more. High AC characters will not get hit as often and they shouldn't.
Match this with attack. At level 5 you want a 50% chance to hit 19 armor so normal attack is +10. That doesn't mean that you need all your guys to be +10. Your boss fight should hit 15-20% more often and random goons should hit ~10% less often. So, your boss should have around +14 attack, while your goons only have +8.
2)Damage vs health:
A group of 9 guys has over double the health of a group of 4 guys the same level, but you can not simply make the bad guys hit twice as hard because the single characters still have the same health. I suggest using some sort of splash damage instead of increasing the same of a single hit. Instead of hitting one guy for 32 hit 4 guys for 8 damage or hit one guy for 16 and 2 guys for 8.
For your magus example I would make the 5d6 damage spread out (fireball strike at 3d6 reflex half?) and take each of his 4 swings against different opponents. While this doesn't make strategic sense it will make game play more fun and players wont feel instagibbed or picked on.
With 4 players action econ already sucks vs 1 bad guy. Each round the bad guy gets 1 turn while the players get 4. This means you need to do more on your turn. Add in another 5 players/turns and you are in real trouble. Agile template has helped with this letting the boss take an extra turn. I suggest giving him 3 turns each round in your case (maybe 4) to balance things out.
It may feel like you are hogging the spotlight when you do this, but that's not entirely the case. Each time you attack/damage a player, they are defending/reducing the damage and thus they get extra spotlight time as well (another reason to spread attacks around).
4)Boss health vs damage
Players are going to front load a metric crapton of damage on your guy, esp if he is a solo target. Ac is not the way to mitigate this damage as it make players feel like they aren't contributing. I strongly suggest other ways of dealing with this to make the fight last a few rounds. Extra health, extra minions to soak some hits, damage reduction, and regeneration/healing are all good options. Another option is someone behind the scenes casting shield other on him (taking half his damage).