Not trying to argue or anything, but I've never heard of anyone EVER sanding basecoat in between layers (I'm talking auto 2k, which I'm sure is what you said you're using). Old School acrylic guys etc will, but wer're not talking acrylics here and its a complete different paint process.
If the basecoat looks a little bit orange peely, not excessive, but only very slightly, which sometimes it can under very close inspection, the thinners in the first clear coat layer should smooth this out anyway. If its excessively orange peeled, then either your technique or gun setup needs a look at. Check your air pressure at the gun (not at the compressor) is correct, check how close to the guitar the gun is, check the gun settings are right, check you're not overlapping your layers too much or too soon between coats, check that you're moving fast enough and the gun isnt being held on the same place too long.
For a solid color like the black you're doing I usually only ever spray two full coats of base and thats after one light tack coat. The time frame for that would be spray tack coat, wait a couple minutes, full coat, wait ten or fifteen minutes, second full coat, wait an hour and then first clear coat, wait ten to fifteen minutes, second clear coat, wait twenty to thirty minutes and then last clear coat. All in one session, no sanding between coats. Let it hang for a week before you wet sand and polish the clear. That is how I spray 2k auto base and clear on a guitar.
I hope that helps you out and saves you a lot of effort in uneeded sanding!