Hey man, I've done this only a few times and I know exactly what you are talking about. Um, I have always just got to that point and stoped, knowing that if I went any further than I would have to do a grain fill coat, so obviously I just wanted to cut some time out of the process. You'll have to be real carefull on the sides and horns though because it's real easy to sand through that clear coat. If you do than I think you might have trouble with the paint soaking into the wood and causing discoloration and uneveness.
I have been told that the absolute best way to do it would be to take it all the way to the wood and start the whole process over, but I just finnished a '68 tele bass without taking all the way down with no problem at all. You should check out Reranch.com they have everything you'll ever need for refinnishing you're guitar, they even have a gallery with a van halen style guitar done with their paints.