Just did a jeep/buggy with 2.5 ton toploaders. Some pics can be seen here if you intersted. pics
As for your questions dont worry about the machining issue. There is an easier way. Let me go down you list though.
1. No machining, Pound out the studs, reverse them. Remove the spindle bolts and replace them with flush mount allen head bolts. You will have to buy a 15 dollar taper tool to get them to seat flush. (buy a good one the first one I wasted 5 bucks on because it sucked and had to go buy the good one for 15. The good one had multiple flutes on it) When you install the tapered bolts use some red locktight. The bolts I used where around 1" maybe 1.25" and used a 7/16 socket/allen wrench to install. Doing this leaves plenty of room.
2. Has been answered. Dualy so it is already short. Flipping the hubs would make it as wide as the front originally.
3. If i was going to do it over and didn't get a smoking deal on the front and rear I would have setup two fronts and made the rear fixed until I was ready to do rearsteer. Although if you get a good deal on a front a rear then pick up the second front later you have spare hubs and a spare chunk which is always nice.
4. The knuckles on the front rockwell can be swapped left to right so you can more the TR behind the axle if you go full hydro which is nice. The steering arm on the rockwell is the opposite of say a jeep because it points in toward the chunk. You can get an after market arm but they are pricey.
5. You will definately need significant antiwrap with leaves. But its been done and it works. The concern is axle wrap and the damage that can be done to the springs and stock hangers due to the weight of the rockwells and the new tires.
6. The rockwells aren't any harder to convert to 4 link than any other axle. Its working with the room and space you have on your current frame that can be a PITA.
7. Definatly think you will want hydro assist or if it is going to be a trail only rig full hydro. I went for full hydro because it was easier and not much more $$ once i sold my old parts.
8. already answered
9. I would just get a fuel cell. It will make it that much easier when you go to 4 link
10. Not sure what you mean. Bump stops in the normal location or there abouts would be good. Probably want some limiting straps
Your going to have to move the front axle forward, which will be some what of a pita because of spring hangers, unless you have a ton of lift which will make your COG probably higher than you want.
Dont waste the money on detriots just weld up the diffs. Thats my opinion. Especially with hydro steering. A detriot is still going to give you a plow effect when your on the gas so you might as well weld the diff and spend the money on the selectable hubs. You only really need one hub too if you can find just one.