God ,I wish I had a few hrs. to go thru this with you. It takes me more time to disassemble a engine that it does to assemble it. Most people just grab an impact and a big hammer and destroy things. Little things that if you pay attention can save you money and end up with a better engine. For instance ,DO NOT go to Harbour freight and buy a number stamp and bang the crap out of the rods and caps. If you do you can rest assured the rods will all need to be rebuilt or replaced. I just keep the caps and the rods together ,it makes NO difference which hole they go back in if they are straight and true. most people will argue with that point. Thats the same thing as saying a crankshaft from one 350 chevy won't fit in another 350 chevy. As long as everything is the correct specs the parts do not know where they came from. Make sure you have gas hose over the rod bolts when pushing them out past the crank. I have seen many cranks need grinding only because the rod bolt threads were banged into the crank.
When taking the rods off look at the bearings very closely, They will tell you by their wear patterns if the rod is bent or needs rebuilt. You did check the side clearance on the rods right? when everything is machined and going back together is the wrong time to figure out end play on the crank, side clearance on the rods ,deck height ect ect ect. Find these problems when taking it apart and you won't have to run back to machine shop 5 times .
Use the same rod and piston and bearing and install on all four corners on the block ,feeler gauge and check the deck height on each corner.This will tell you if the block needs decked and how much to take off. Check main bearing very carefully and you can tell if you need a line bore on the mains.All head bolt threads need to be run when disassembling ,If you deck the block that means your headbolts will screw farther down the hole. If those holes are full of Rust the torque rating will not be correct. TAKE your time and don't destroy things . you would be surprised how much damage you can do without even knowing it.