I'll answer in order:
I'm with you on the pickup placement.
Yes, the Inazuma is 2nd run. I don't believe you have to remove the pickup though. There should be enough room between the neck and front pickup to adjust it or, mine has a bullet style truss rod that adjusts at the head.
RS 1st run:
http://www.matsumoku.org/cm_models/2021 ... first-run/RS 2nd run:
http://www.matsumoku.org/cm_models/2021 ... econd-run/I don't currently have a playable CS but I don't remember it being neck heavy. I also built a guitar that is basically a CS with more cutaway in the lower horn for better fret access and it doesn't neck dive. It's close but it's also only 2 1/2" thick so it's pretty light.
I've never owned a TS but I believe you're correct. The body is a touch more "strat-ish" which probably helps in that area.
Now, by non-trem PE series, I'm guessing you're talking about PE-60, PE-R60, PE-R80 and such?
They're very nice "Les Paul-ish" style guitars that I believe are as good or better than LP. Just my opinion but, I've tried many a time to own a Les Paul but never found one that felt good. My PE-R60 is fantastic and it's not even the top end for the model.
Sadly, I sold my PE-R80 back in '94. . .
EDIT - Personally, I do not like the neck joint on a PRS.