Your description sounded a lot like a balance issue.  When it is pure driveline angle, it is usually worse under acceleration or deceleration, not both.  When you said it increased with speed and and was still there when you put in the clutch, balance would be the first guess - as your inspection has proven.  Unbalance forces increase with the square of the RPM of the driveshaft so the forces imposed on bearings and seals can be pretty substantial when you get to higher speeds.

With leaf springs, you usually want the axle to be about 1/2 to 1 degee "lower" than the driveline - if your driveline is at 3 degrees, the pinion is often set to 2 or 2-1/2 to allow for the wrap of the springs under acceleration.  If set your pinion closer to 6, your angles at each joint can start to climb so even if the pinion and driveline are parallel, you can still be putting high stresses on the u-joints.  I like your idea of raising the the rear of the trans up.  I ran the numbers a few years ago when I was installing the TKO and you may need about an inch.  Start with 1/2" and make sure nothing is hitting and get a digital level to check everything.  I got a Sears/Craftsman unit for about $29 and it was one of my better tool purchases.

Try to bring it up to 5 degrees rather than the full 6 to allow for wrap.  Even 1/4" at the trans will help and if there is some tunnel in the way some gentle persuation may give you a little more clearance.  If you can get the car on a lift, measure from the front u-joint to the floor or base of the lift, and the same measurement to the rear joint and then measure from joint to joint.  Post the numbers and we can figure out what your actual u-joint angles are.  There are some good sites that list u-joint angles versus max reliable operating speed.  As angles go above 2-1/2 if I recall, the max speeds drop pretty quickly.