What I would do...
Pull the shims
Install doubler (custom crossmember, long slip CV driveline up front, shortened rear, and so on required)
Check pinion angle with doubler, new drivelines, and no shims
Go from there.
I wouldnt modify an already "proven" spring pack - yet. I have a feeling that without the shims, the space between the tie rod and springs will open up a lot since they're rotating the front of the axle down to bring the pinion up, thus pushing the tie rod down towards the springs. Also, if you get a drop hanger built for the front, it will lower the front point on the springs, which will change the way the axle sits too.
Think of a rocking chair, one end of the rockers on the bottom is the spring hanger, another is the shackle. As you sit on the seat, the pinion is level and youre straight up and down. Now, with longer shackles like you have, that would be like rocking back on the chair. The pinion is pointing down now because that part of the spring is lower because of the shackles. Put a drop hanger up front, thats like rocking back forward again, its bringing you back closer to level. Get it?
Im not saying a drop hanger will solve your problems, but I think between not running one, and the shackles, thats a big part of your problem with the pinion so low.
Youre already committed to dumping money into it now with the doubler setup for the new crossmember, drivelines, floor mods for the new shifter, etc. So, in my opinion it would be plain dumb to not install a new front hanger too at this point.
~T.J.