Hotchkis spring installation....

Is there more clearance at 4" ? If so, run it at 4". IMHO, you'll need the extra ground clearance anyway. Then, grind some clearance into the back edge of the shackle bars.

...Next check pinion angle when the car is together with the weight (engine) in it.

Yes today I got it in the middle hole. The center to center measurement is 3 3/4", so almost close to the stock shackle length. After doing this, I do have a touch more clearance, and I suppose I could grind some clearance in the back edge of the shackles for more wiggle room.

I think I will run into the same problems as you if I use the supplied Hotchkis front spring mounts. I also have TTI headers and 24.5" diameter tires all the way around. I kept the stock front hangers in there.