Hello kgk, I am having the same problem. What did you end up doing to fix this?
When I owned a JEM JR I would just adjust the classical position with the neck steeper closer what a true classical guitarist would sit so the tip of the headstock was at or slightly below line of eyesight.
It’s great jack placement for not breaking cables live but it’s kinda terrible for sitting. Especially as mine was severely recessed so right angle cables were out of the question for the most part. The way Charvel does it is a much better solution imo. (I think Leo Fender got it perfect on the strat to begin with so why reinvent the wheel, but whatever).
More often than not I would just use a strap to bring it higher up on my body.
I also have one of those footrest things they use. Or I rest my left foot on the top of the side of my right foot for elevation if you dont press down its okay but this can get uncomfortable after a while. See below pic for example. (A stack of textbooks is a great poor man’s version of this, btw)
I will probably stick with a 90 degree cable but will explore some alternative seating positions.