1. I've never seen a 12L3 come with two sets of angled upper arm mounts, could you take a picture by any chance?
2. The shock needs to be long enough that at full extension the rear pod droops just slightly below level. If your pod droops more than just a little bit, shortening one ball cup would be the solution. When the car is loaded and at rest, the pod should be level to the chassis, but when you lift the car, there needs to be that slight droop.
3. It's tough to get a stock motor geared correctly in the 12L. There isn't room enough to run the pinion you need. There are several solutions: Kimbrough makes a set of rear bearing holders that are offest to move the rear axle back a bit, creating more room for bigger pinions, and several companies (IRS comes to mind) offer replacement rear pod uprights that move the axle back a bit. The other solutions are to run a smaller spur gear, or to shave the TBar slightly to allow the motor to sit further forward.
I prefer the smaller spur solution, I don't care to shave my Tbars, and I feel that moving the axle back could adversely affect weight distribution.