1 and 2 essentially have the same answer. By lowering the suspension, you have changed the steering geometry. The only fix will be to correct the geometry back to stock, usually be altering the steering arm to make the drag link parallel to the springs as it would be stock.
3 there really isn't any easy fix for, other than putting the leaves back in the spring pack. By removing the leaves, you have lowered the spring rate in addition to lowering the ride height. With the lower spring rate, you have made it easier to bottom out. With the lower ride height, there's less distance for the axle to travel before it hits the stops. You might be able to trim down the stops to get a little more clearance, but that really isn't the ideal solution.
The best overall solution, which can correct all 3 issues, would be to reinstall the leaves in the front, and use a dropped axle and corrected steering arm from
Sid's.