ive seen a heimer before in a very long game stack 5 afchangel's staves for 15% mana to ap once, while it made him unstoppable, i couldnt help notice the +1000 mana effect was unique, lowering the effect somewhat

TECHNICALLY manamune and the staff have different unique specials that give +1000 mana, does this mean they stack? or will one still only get 1000 mana from abilities?

They do stack.
If you're willing to sack some survivability on some spell spamming champs, these two items are a really fun combo.

They make AP Kog look good again.

Do they? I'm given to understand that the +1000 mana cap is shared between the Tear "family" of items, but I'm also willing to admit I haven't tested it.

The 1000 bonus mana does not stack. Tear, Archangel, and Manamune all share the same 1000 bonus mana pool.

but both bonuses apply?

Tear, Manamune and Archangels specials do not stack. The 1000 bonus is shared and so is the 4 Mana per spell cast, i.e. you still get only 4 Mana per cast towards a total 1000 bonus cap even if you have both of them.

This is not theory - I tested it recently on Veigar when manamune first came out.

they do in term stack, if you were not aware they are both unique passive, but on different items. different items that have a similar unique passive stack. you will have a mana pool of bonus 2000, I have tested this on gragas.

then how come when you use an ability, you dont get +8 mana, if they do indeed stack.

I assume both the bonus damage and the bonus AP take affect though, it could be a really strong combo on Kayle due to her new passive (it still feels new to me, the bubble being her ultimate feels new too!)