Applying the glue leaves a nice shiny surface appearance. If you notice any part of the piece that appears dull in contrast to the rest you might have sanded through. I typically go straight to micro mesh after about 6 coats of thin CA, sanding for about 10 seconds for each grit. I never go through my finish unless I intend to.
Sand through occurs for two basic reasons - 1. in experience on how much to sand and 2. Not enough CA or other finish. One can put 30 very thin layers and still only have .005 or .007 thickness of CA. I only apply two or three layers and have a build up one .01 to .015. How do I know? I measure it with calipers. If you don't have a set of calipers, get a good set from Harbor Freight or other place.
Measure your blank just before you start to finish and write it down. Then add your CA and measure your thickness build up.
This is me personally and the majority of people apply CA probably the same way you do - with paper towel. I do not use paper towels to apply CA. I am not a scrooge but using paper towel (PT) is a waste to me, as the PT absorbed 75% or more of the CA with only 25% or there about getting onto the blank. No big deal but something to think about.
It is fairly common for those new to pen turning to sand through and it is primarily because not enough CA thickness is getting onto the blank. Calipers can help with that and it will help you in measurements for fitting you blank to the pen parts. (Don't use the bushings for the measurement of sizing the blank when turning of finishing. Use measurements with calipers.)
My latest (#5) was from a spotted cherry blank. I used GluBoost again but this time I wet sanded with MicroMesh. On my final pad my blank showed a whitish spot. Went down a grit and it got worse. I'm assuming I went through the GluBoost???
I re-applied several coats of the thin GluBoost and after MicroMesh and buffing all was well. My best looking pen yet!
Mike, Is that a South American cherry? I grew up with North American (South) cherry wood and made several pieces of furniture from Cherry, and that looks very grainy for the kind of cherry that I have used.
If you aren't sure what "sanded through" looks like (or you feel nostalgic and want to see it again), then make a pen, but:
Turn the basic pen blank to a cylinder.
Finish it with your favorite CA finish.
Sand a part until you've sanded through.
Feel it, smell it, take measurements, learn from it, whatever you need.
Practice fixing the sanded-through part if you wish.
When you're done working on the sanded-through part:
Turn off the finish.
Turn the pen down to the proper size as you would any other pen.
Finish it right, but don't sand through.
This method is a great way to learn how to do a consistent, high quality CA finish. Finish the cylinder, turn off the finish, repeat. When you get close, then do the final turning and finishing for your pen. Repeat on your next pen until you reach a high level of dependability and confidence. Great practice!