There is no reason to put one dime into JB3/JN3 brakes. They're the *********, smallest, least-powerful "power" brakes ever put on a GMT400 vehicle.
Find a Treasure Yard, locate an extended-cab or newer regular-cab GMT400. Grab the entire front suspension, the booster, and the master cylinder. Now you have "spares" so you can rebuild the control arms, replace damaged CV shafts, etc. and get them ready before you rip your truck apart. Be careful with the lower control arms--the torsion bars on my truck and on the Treasure Yard truck were seized in the lower arms. If yours are seized, you can rebuild them "on the vehicle" with new bushing and new ball joints...but don't put new parts into the Treasure Yard lower arms until you're sure you can get the ones on your truck freed from the torsion bars.
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When it was me, I pulled the calipers apart for cleaning and inspection. There was nothing really "wrong" with them, other than a bunch of hardened crust on the square-cut seal which made the pistons stiff to move, which I scraped-off with my fingernail. Cleaned, inspected, lubed, put 'em back together, they work great. However, the Treasure Yard calipers and master cylinder would also make fine "cores" if you'd prefer to buy rebuilt calipers/master cylinder.
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I re-used the rotors and hubs/steering knuckles from the extended cab. I'm told that the knuckles are the same, but the hubs/bearings are different. I did not confirm that, but a few minutes looking at the NAPA/O'Reillys/AutoZone/etc web sites would list the part numbers for the hubs.
The extended cab/newer regular cab brakes are JB5--thicker rotors, bigger pistons in the calipers. Along with that, the booster is more powerful and the master cylinder bore is bigger.
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The JB5 rear brakes are the same as JB3/JN3. In other words, the rear brakes are garbage. 254mm (10-inch) leading/trailing drums. The best option is to figure out what gear ratio you have, then find a K2500 9.5" ring gear 14-bolt, semi-float axle assembly with the same ratio and 6-lug axle shafts. That will have 11.x-inch Duo-Servo drums, and be about twice as strong as the crappy 8.5" ring gear axle that's probably in there now. The rear brakes make at least as much difference as the bigger front brakes. The 254mm drums are terrible.
Together--the JB5 front brakes plus the bigger 11.x rear drums gets you the equivalent to JB6 brakes. Which is what I did on my '88.
Note that my brake upgrade was part of a front-suspension rebuilt including lower ball joints, and Polyurethane control arm bushings. My tie rod ends, upper ball joints, idler and Pitman arms were fine. My truck didn't come with a front sway bar, so that was grabbed from the Treasure Yard truck as well. I used the Treasure Yard brake pads which were almost completely worn-out, for about a week to take the rust off the rotors, before I put "good" pads on from Performance Friction (Made in USA, in one or the other of the Carolinas.) It also got fresh brake hoses from Russel; although if I were doing it again, I'd use the hoses from Classic Tube, which will almost-certainly fit better.
www.summitracing.com/parts/cst-sbh6055
Free Shipping - Classic Tube StopFlex Brake Hose Kits with qualifying orders of $109. Shop Brake Hoses, Sets at Summit Racing.
www.summitracing.com
The RWAL unit on my truck has a cast-iron body with it's own bleeder valve. Yours is the aluminum body with no bleeder. Be sure to follow the Service Manual procedure for bleeding your brakes.