It all depends on the look you went. I kept the stock S-10 diff in my '46, but I have 15x10" wheels on the back with 3-3/4" backspacing, and I have tubbed the box. If I were doing one with fuel injection I would actually scrap the stock S-10 harness, and use a painless fuel injection harness along with the painless chassis harness. This will save you a lot of headache in the long run.
Start by stripping the S-10. Get the body and everything you don't need off the frame. Don't remove the body mounts. Yet. I think the EZ chassis swap makes it much easier if you're looking for a not-too-low ride height and aren't experienced with fabrication. We've never used those kits, but we've always wanted ours lower than was possible with the EZ kits. I've never done the S-10 swap with the stock S-10 driveline, so I am not sure how your cab placement will go with the motor in the stock location. We've done it with big block Chevy's and Big Block Buicks and the motor ends up in a different place depending on the cab style being used. On my dad's 52 Chevy with a 454 he used the stock 4.3 motor mounts and it worked out just right, so the 4.3 might be in an okay spot, but you'll find out.
When we set the body on the frame we set the cab and front fenders/grille as a unit, so that you can clearance the areas you need to, as well as to make sure your tire ends up in the spot you want in the wheel well. Always mount your cab first, then you can disassemble the front fenders afterwards if desired. Then do the running boards/bed at the same time.
When disassembling the S-10, work the other way, take off the box, and work your way forward, etc. If you're wanting to lower the S-10 frame, do it before you mount the body, and then put similar sized tires and wheels on to what you plan on running (at least in height) before you mount the body, so you can get the ride height where you want it. It's a process, but if you do it step by step it's pretty easy.
