To RJ, Every paint has a data sheet that will tell you the recommended dry time, and time to overcoat your base with clear. In the absence of a data sheet, the general rule is no sanding between. After you spray the base, allow at least 30 minutes for the base to flash, and then come right over with the clear coats. Most paints tell you the clear must be sprayed within 24 hours of laying the base. If you go over the 24, then it's recommended to respray.
Now, that said...I have many times layed a base coat and then taken a week or more to airbrush a mural...and then sprayed the clear without any further base prep besides a good cleaning with a tack rag. So, while there is "perfect" technic...there is also a wide margin with modern paints.
KV...if you have enough clear left, you should be able to get rid of the scratches using 600 grit (and plenty of water to ensure you don't introduce any more scratches). When you learn to pay attention, you will immediately learn the "feel" of the paper when grit is trapped under it. It gives what I would call a "rolling" feeling, instead of the sliding feeling you need with a clean sheet.
With good buffing compound you can buff right over the 600 grit, or if you want to speed the buffing, work the surface back gradually to your 2000 in steps. For example, hit the areas with scratches with 600, then go over that with 1000, then 1500, and finally 2000. If you buff the 600 surface it just takes longer with the buffer.
Oh, the buffer of choice for big jobs is the big rotary 1200/2400 variable rpm models. If you are using the smaller orbital buffers...then it takes triple the time to buff, so I would definitely choose to work the surface back to the 2000 grit before trying to buff.
Of course, if you cut through the clear with the sanding or buffer, you will need to respray...at least the clear if not a thin coat of base and then clear. It hurts, but it happens...even to the best when $#!t happens, and $#!t frequently happens with paint and body work!?! If I have an issue laying the clear...like say a run develops or I got he temp wrong that resulted in orange peel, then I will lay an extra coat or 2 of the clear. That gives me more thickness to ensure I won't cut through the clear when I am fixing the blemish in the clear.
If you have a blemish in the base...don't think the clear will fix and/or cover it. Stop, let it dry, and start over. Treat the first layer of base as an "extra" primer coat. Again...paint and body work is fraught with minor set backs. No matter what, don't fall into the mindset of "that's close enough". A few extra hours redoing a job now will save you a decade of seeing the blemish every time you walk up to the car and your eye always goes straight to it...followed by the thought of "I wish I had taken a couple extra hours to fix that when it happened".