VPI 3D tonearm adjustment

I have a couple of questions on set up of my new Prime and the 3D tonearm:

1. I've had the TT for about three weeks. I had a scout and moved my Dyna 20x2L to the Prime.
my first impressions was this is a wonderful upgrade. But after a couple weeks I noticed there was more glare on the highs.  I initially set the tonearm parallel to the record - dead level. I then ran across articles about how on some earlier 3D arms the shell warped. I think I have a new style arm, but last night I decided that rather than set the arm parallel I would check and make sure the shell was paralelle - it was not. It tilted downward 1.5 degrees. To get back to paralelle had to turn down the vta adjustment to where the body off the adjustment tower is almost all the way down. But with it adjusted as such the sound is now fantastic. My first question is the shell supposed to be parallel?

2. My second question is now that the tower is almost all the way down I can't use the alighnment jig, the tonearm hits it.  I've heard that the small cup on the underside of the tonearm where the needle sits,can be raised and lowered - is this true for the 3D arm?  There isn't a screw on the top of the arm to adjust with?