The spring over in the front is much easier to do than the shackle/spring mount flip in the rear. It took me a few hours to do the front and almost a whole day to do the rear. The main pin for the front rear spring mount goes through the frame and is welded onto a plate that is inside the frame. Once the rivots are drilled out, the welded pin has to be ground off from the inside. The gas tank may have to be removed to do the driver side; I don't remember how much room is there, but i'm pretty sure that it will have to come off. One other thing that you will have to do is re-drill a hole lower in the frame because the main pin is offset from the bolt pattern in the mount. As to axle droop, I removed 3 leaves from the rear spring pack starting with the smallest and then ever other one and the truck seems to flex just fine. I did not measure axle droop before the springover and shackle flip, but I do know that it flexes a whole lot more now than it did before.
The front springover is pretty easy. Just weld on some new perch mounts and move the springs. The steering linkage will need some modifications. Look for the "springover" post in this listing from a few days ago, and that will give you a good idea of what needs to be done.
As far as the tranny, I think that it is a matter of preference. I know two people that have done 350 conversions. One stayed with the original manual tranny, and the other went with an auto. Both trucks had 40 + inch tires and ran 70 mph with no problems. If you decide to go with the manual tranny, you need to buy an adapter so that it will bolt to your 350. Check with Advanced Adapters, I think they have these adapters for $400-$500.
Hope this helps !

Jeremy