Mimi,
On all natural granite tops there will be some imperfections like tiny pits or possibly hairline fissures. That is the nature of the stone. It is NEVER like a sheet of glass. Part of the reason for this is granite is made up of 7 components, the three most common are feldspar, quartz and mica. When they flat polish the face of the slab at the factory they tend to pull out some small pieces of mica during the polishing process. That's what the pits are. If there are hairline fissures (they look like spiderwebs when you look across the slab with your eye level just above the slab) that is also a natural occurrence that you see on some granites.
I have run into this grit a few times. Before you do anything try buffing the counter with fine steel wool and then wet vac it. According to the MIA it is swerf that got stuck in the stone. Try wet vacuuming it out and see if you can keep the grit down to where it is a couple of weeks before it reappears. When you get it to that level we will strip the sealer and topically apply a water based resin that will impregnate the stone and act as a barrier to the grit coming through to the surface. Keep in touch with me on that.
The fissures can be treated with Pectro to hide them. Here is a link for that:
http://www.defusco.com/Glues:-Epoxy,-Polyester,-etc.-Waxes-&-other-Stone-treatments/c82_505/p2303/TENAX-PECTRO-BLACK-STONE-TREATMENT---1-LITER/product_info.htmlWhat do you mean by "water marks"? Could you give us some pictures? You can always repolish the granite with a polishing compound and that will enhance the gloss level, but if the water marks are stains and you sealed over them you will have to remove both the sealer and the stains with an alkaline solution. Get in touch with me here or call my office at 800-289-6834.
Glad to be of service,
Mark