I've read back through the diary but still I'm unclear on what your base coat and clear coat materials are.
Acrylic lacquer? Acrylic enamel?
And in one post I got the impression you were going to use polyurethane (Cabothane) as the clear on the body.
If you put poly over lacquer there will definitely be a problem, and enamel won't play nice with poly either.
I also think I read that you wet sanded the primer (at least that's how it read to me). Not really common practise, but that would lead to potential adhesion problems not a soft or uncured finish.
FWIW, the last build I completed (blue metallic strat) I sprayed acrylic lacquer base & top coat (via gun) let it hang for 4 weeks before level & polish, assembled and set up, all good. Then I noticed an indentation where it had been sitting a stand... WT???
I left in a neck hanger for a few more weeks (took it down to play it once in awhile) indentations were gone and now it's hard as rock.
Not sure why this happened as I sprayed while the temps & humidity were as close to perfect as it it gets in the year and I used my usual thinners and mixing ratios. For whatever reason this one took 7-8 weeks to fully cure.
Sometimes "stuff" happens.