A 3" shackle lift requires a 6" shackle extension, and when I say extension, I mean the shackle needs to be 6" longer than whatever is there now - the problem with long shackles is that they flex "side-to-side", reducing the "lateral location" normally provided by leaf springs, making for a very unstable vehicle, and one in which you could possibly find yourself with no steering, as when you turn the wheel, instead of the drag link pulling/pushing on the knuckle and turning it, the entire axle moves sideways and the vehicle continues to travel in the same direction.
You also need to recognize that the engine you're about to drop in weighs close to four times the weight of what you're taking out - you're going to need more than a shackle lift to compensate for that.