If you really want help with a plan of attack, I'll give you some suggestions:
0.
Start a build thread in this forum - Take some BEFORE photos. Everyone forgets to do this, and the first photos we usually see are of a dismantled truck. It's going to be good to see how far you've come since Day 1, so take the photos NOW and get them online. Post photos of the various aspects of the build, and if we see mistakes we can help you get back on track... if we know of faster ways to do things we'll chime in with ideas.
1.
Prep all new parts - It's going to be a LOT easier to do the work on axles and anything else while they're out of the truck. If the D60 hasn't been rebuilt, now is the time to replace seals, kingpin bushings and any other worn parts. You might as well (ooops, there's that expression again) deal with your steering solution before you install it, so buy the crossover arm (or dual arms if you want hi-steer) and install them now. Then give everything a good once-over with a wire brush and a fresh coat of paint. It feels a lot better to see new parts under your truck when they're freshly painted....and it looks nicer in the photos that we will require you to post.
2.
Axle swap - I'd probably do that next, since it's a good confidence builder and won't take as long as a driveline swap. You're going to need them in position to measure for new drivelines at some point anyway. Now might be a good time. You can also put the tires on the axles to see what sort of wheelwheel clearance issues you have. Out back you'll probably find that the axle is too forward in the wheelwell, and you'll want to add a zero-rate block or build a custom offset springperch to compensate. Up front, well you're kind of screwed no matter what you do because the front tires need a lot more clearance than the rears....
3.
Driveline swap - You'll probably be a lot happier at this point if you put on a set of small tires/wheels or pull the wheels completely and rest the axles on small jackstands. It's not much fun doing an engine swap on a lifted truck, and you'll find that the engine hoist probably won't go high enough to clear the frame unless you take some proactive steps. Pull the front clip off before you start. It's only about a dozen bolts to remove the entire thing as a single unit, and it will be SOOOO much easier to work on that way.
At this point, your biggest issue will be valvecover clearances, and maybe distributor clearance....the header tubes may require gentle clearancing of the upper frame rails too. For the initial install, it will probably be smart to avoid getting too tricky with trying for the "flat bellypan" effect. Just clock the Atlas the best you can: having a HP60 vs. a standard pinion is going to give you much better front driveline angularity, so you can probably clock the Atlas flat without binding the front u-joints on droop.
4.
Crossover steering and new driveshafts - Finish up the crossover steering project with a 2WD box (hydro assist too if you want it) and a new draglink. Take your final measurements for driveshaft lengths and call up your favorite vendor for some beefy ones. With all that power and traction, you'll need something a lot better than stock.
Of course the "Might As Well" temptation will sneak in along the way, and you'll need to decide if you want to indulge it. When the engine is out, it sure is a convenient time to repaint the firewall and front framerails with a fresh coat of paint. And with the axles out, it sure would be easy to pull the springs off and give them a quick coat of paint also, and maybe some new poly bushings.... Come to think of it, some of that wiring under the dash isn't looking all that good especially compared to that new fuel injection controller you just installed there
The hardest part is realizing that no matter how MUCH extra you try to clean-up as you go, there will still be things you'll change later on. I don't believe there is such a thing as a "FINISHED" truck build.... you can easily address the weak points, and build a solid foundation, but there will always be smaller things that you'll want to modify and change along the way.
