I was thinking of putting some nice separates in and maybe a small amp (I have a non Bose)

Anyone know what size fits?

Stock woofers in the front doors are 6", so most aftermarket 6.5" separates will fit. I installed Dynaudio system 240 separates, which have a 7" woofer. The width was tight, but cleared all door braces and required no cutting. The Dyn's fit because they are average depth. Some, such as Focal's, are quite deep and event the 6.5's might be tight. Find a good install shop, and not just some "trunk of funk" sub shop, or you'll likely be dealing with door rattles before long.

By the way, the Dyn's are superb. I have them mated to a Microdimensions 75w x 2, mounted under the tool kit in the bracket for the cd changer. I do want to try turning off the Bose filter by vag at some point, also.