Do percentage bonuses stack?

Yes the bonus's stack,though during combat they do recharge just a little more slowly then when out of combat but with higher stats like your using you won't notice the slow down really. It's a very good way to have an almost limitless supply of magicka. the stacking works different for magicka regen as opposed to say weapons and such. here are a few links to other such stacking...

How does multiplying damage work in Skyrim? for damage multipliers

https://gaming.stackexchange.com/a/38363/15734 carry weight speech and such

http://www.uesp.net/wiki/Skyrim_talk:Enchanting broad base

hope this helped

I'll specifically address the bounty comments.

Are there differences between stacking perks, stacking enchantments, and stacking a combination of the two?

Yes.

Perks stack multiplicatively with themselves, so for example the "Agile Defender 5" perk, which increases Light Armor rating by 100%, when combined with "Custom Fit", which increases Light Armor rating by 25% when wearing a full set, will result in a 250% total increase in Light Armor defense.

On the other hand, enchantments and potions use the same effect, which you can see under the "Active effects" tab in the "Magic" menu, and they will all stack additively with themselves. So for example a "Fortify One-Handed" enchantment with 20% strength, when combined with a "Potion of Fortify One-Handed" with 40% strength, will result in a 60% total increase in One-Handed weapon damage.

These two categories stack multiplicatively with each other, so drinking a "Potion of Fortify Archery" with 50% strength while having the "Overdraw 5" perk, which increases Bow damage by 100%, will result in a 300% total increase in Bow damage.

AFAIK bonus stacking in Skyrim should be additive. For example if you have x Magicka regeneration rate and both +50%, +70%, you'll end up with x*(120%) so x*(1 + 1.2).

This game should not be like WoW were stacking of % based is usually multiplicative (i.e. 50% + 70% in multiplicative is 1.5*1.7 = 2.55).

Hope this help, Cheers