Speaker size, Yes I've searched it up.
 

I've looked everywhere, whats the best speaker size, as I am debosing. I'm ripping the whole system out and putting in aftermarket speaker and head unit in. I have the head unit and everything already. Just need to go get a proper speaker size. But I know the bose have a special one.

Someone who has done this, please oh please point me in the right direction. Its a 99 RS

If you're upgrading you'll have to remove the bose completely, as opposed to adapt it.
You'll need front and rear speaker brackets. The front's are 6.5" and the rears are 6x9".
The fronts are produced(http://www.car-speaker-adapters.com/items.php?id=SAK068).
But, the rears are NLA as far as I know. You'll likely have to get them second hand.
Depth can be an issue in the front. Most stuff will fit, but if you're going for power a huge magnet may bottom out.

What's the size of the speaker inside the top of the dashboard?

I don't know, but I would just remove it and put the cover back. Not many people run a center channel in custom car audio setups.

Ok thanks

Thanks a lot for the reply!! I'm pulling it out tonight and seeing if I can fab that pvc adapter myself. I'm not going for big power as the car is tiny and doesn't need so much sound.

If I were to put a custom audio in my Bose setup I'd still keep the rear snake as it is (as I really like the soft bass it produces) and upgrade the door speakers only, also instead of using a full size amp I'd go with a small power pack (e.g. Alpine KTP-445U) which would be more than enough for two channels one per door speaker.

Nobody has really been successful at retrofitting speakers into the Bose tube. You might be able to restore it from a pile of original parts, but replacement speakers do not work very well.
A couple of well powered door speakers would be more than enough for the small cabin, so long as you're into stereo ;)