HB32- (nice handle-what body?)
It is not critical for the pitman arm to be level. The tie rod and drag link should be parallel, and in the same plane front to rear. This is at ridehieght, with the wheels centered. As for the geometry changing during movement, it does. The idea is to elimate bumpsteer, which occurs when you are traveling in a straight line and encounter a bump in the road. Not when the wheels are already turned.
You say the ball joint end(forward end) is higher? That seems rather odd, as generally the end of the pitman is tipped down. Do you have the chassis at the approximate ride hieght? The input shaft of the box should be angled up toward the firewall. If it is angled down, you will need 3 U-joints(and a sperical support of the floating shaft), which is really odd in a small block Deuce.
As for the box hitting the mount, depending on the style of mount you are using, you may have to trim/relieve the mount to accomodated the box. You will need to add additional gusseting or support to the mount where you cut/trim the existing mount.
Let me know how you get along, I've built over 100 '32 chassis, with SBC, Ford, Nailhed, Hemi, pinched, kicked, IFS, IRS, etc - Happy to help you where I can.