I think you are right in your thinking weirdy, it looks like you sanded after the timber mate up to 600 grit? unfortunately the DT stain coats will not soak in enough as there is not enough "tooth" in the timber especially the maple neck. I would sand it no more than 320 grit on the body and 240 on the neck.
You should be able to get the maple neck darker than that creating a bit of tooth by sanding with 240 and then re-staining. I'd probably do more like 4 stain coats and 4 intensifying coats.
I never use steel wool on DT anymore. I think there is petroleum substance in it to prevent rusting which reacts badly with DT. plus its messy. a bit of 1200 grit & 2000 grit wet & dry on the intensifying coats and final coats (no sanding required in between stain coats) will work wonders lightly sanding with the grain in one direction once cured and before applying the next coat.
Let me know if you have't read my previous posts (somewhere in this forum) about applying ultra thin coats of intensifying coats and finals which aid with curing faster and non streaking.
BTW are you using DT neck finish coats on the neck or just general finish coats?