Well joe , looks as though a phone call the machine shop will be in order. If the mains and connecting rod caps were mismatched prior to your disassembly , block will need to be align bored and the rods resized and this will mean oversized or custom bearings but the bearings are no big deal , it's the machine work expense , as you know. Got to sort that out before bearings are ordered , that's a must . I know you want this engine , and the whole jeep for that matter , done right , so , at the minimum , all parts of the rotating assembly ( rods and main caps ) will at least have to be gauged . But usually this works out to the align bore job and resizing the big ends on the connecting rods . I know you'll get your prices first but your machine shop guy is really reasonable and that's great ! Machine shop work is always known to be $$ .
I knew from the earliest pictures of the engine that work was done to it but this time around you'll get it right . No fear . I'm sure the shop will stamp the block and mains , rods and caps correctly on one side to match for future disassembly if needed . Always good if you decided to replace bearings with the engine in the jeep and the oil pan off to do a fresh up bearing replacement . Happens more often when a manual trans is used . Bottom ends just work a bit harder with a stick . You'll definately want to plan ahead for this and be ready for that future swap if need be .
Once the gauge and/or machine work is all done , the plastigauge will have the final word on calling it good or not. When properly cut and sized , the only adjustment is bearing clearing clearance and sometimes you got to over or under size if need be . But we'll see how that works out , possibility since this engine had some work done before . But maybe we'll get lucky .
I got faith in your machinist as long as your happy with him.