One of the first 4.0's I ever opened up the bottom on (a long time ago). I started my standard procedure of stamping a dot into the left side of the cap (same thing I do for a piston pump or whatever). One dot for one, two dots for two, until I ended up with a circle of six dots on six. About half way through the job (oil dripping in my eyes), I noticed the number on the cap, then thought, well I'm wasting my time, then saw the same number on the next cap (think it was three) and then thought, I'm not wasting my time after all.
Not sure about the 4.0 though in most all motors, the connecting rod is cast and honed in one piece, the end cap sawed off. I've actually been able to match the caps with the rods using a magnifying glass, metal dye and matching up the saw marks, good eyes and a little luck. Maybe not necessary but who knows if they were sawed off in exactly the same spot or not, if the honing process was absolutely true or not, 0.008 doesn't leave you a lot of margin for error? The guy who made that rookie mistake thanked me profusely. Though the book does say you can mismatch the bearings to get the desired clearance, so the hone may have a slight allowable error margin.
I never really worried much about the balance in most motors. Tried to find out if they were internally balanced or externally balanced, kept the proper flywheel or torque converter with the externally balanced motors. A torque converter full (of half a dozen quarts of oil) has to have more affect on balance than does a couple of grams on a connecting rod.
Best basic tip I can give you is, too tight will kill a motor quick (heat expansion and friction), to loose my be noisy but will usually outlast too tight. Plasti gage is pretty good stuff, take your time, do it twice, top of the bearing and bottom of the bearing. Clean the oil off first, oil melts plasti gage.