The good news is that you've decided you want to rebuild whatever box of pistons and rods it is that you just blew into crumbs of metal. The bad news is that you've got no idea what you're doing. Lucky for you, all you really need is the ability to comprehend that service manual of yours, the capacity to handle a torque wrench, and your readiness to follow these here tips.
Clean everything, and then clean it again
If you've somehow spent less time degreasing and wiping down all of those grimy engine bits and oil galleys than you have actually bolting everything together, then something's gone terribly wrong. Microscopic particles of dirt and machine shop leftovers are enough to take out engine bearings, cylinder walls, and ultimately your whole engine.
Balancing the assembly
Chances are, once you're engine's been disassembled and you've got whatever pistons and rods you plan on stuffing into place, you'll be dropping the whole shebang off at your local machine shop. It's there where you'll have the entire rotating assembly balanced to avoid excessive weight being thrown around in the wrong directions at high engine speeds. You know you've found the right machinist if he bolts the crank, flywheel, clutch pressure plate, and crankshaft pulley together as a unit when doing all of this. The pistons and rods have got to be done separately but are just as critical.
Micro-polishing the crank
Your crank's journals look fine to you but they aren't. Microscopic nicks and scratches mean your engine isn't going to last the 200,000 miles you think it should. It's your machinist's job to smooth them all out to a mirror-like finish and make sure they're as round as they were the day your car was first put together.
Honing the block
The texture of your engine's cylinder walls will determine all sorts of important things, like how long it'll last, whether or not it'll burn any oil, and whether or not it'll reach its full potential on the dyno. A good machinist will want to see whatever pistons you've got and know what sort of rings you'll be using in order to achieve the right bore size and finish, which is typically a fine-grain cross-hatch pattern.
Decking the block (and head)
If you don't like blown headgaskets, then you'll want to pay particular attention to making sure both your block's and head's surfaces are completely flat. Use a metal straight edge and a feeler gauge to determine how warped they are or just hand them over to your machinist and have him lop just a little bit off of both of them. Be sure to take into account the increase in your engine's compression ratio based on how much material's been removed.
Gapping the rings
It's your pistons' rings that keep cylinder pressure above themselves, in the combustion chambers, and out of the crankcase. Whoever sold you those rings, though, has no idea exactly how big your cylinders are or how much pressure you plan on generating inside of them. It's your job to figure all of that out and to file down those rings accordingly. Most rings include guidelines that'll let you know how much material ought to be removed based upon bore size and cylinder pressure.
The valve job
You've gone to a whole lot of trouble to make sure cylinder pressure stays where it's supposed to; now make sure it isn't able to seep past the valves when you don't want it to. A three-angle valve job ensures all of that'll happen and eases the transition from the ports into the combustion chambers. The right valve job can reap many of the benefits that a high-dollar ported head would but for a whole lot less money.
Commission the right machine shop and you checking tolerances will be mostly a formality. Still, even the best of machinists have bad days, which means you ought to double-check your engine's cylinder bores, crankshaft journals, rod journals, and deck height to ensure proper oil consumption, compression, and clearances. You'll need specialized tools to do all of this, like the bore gauge and micrometers that you don't have.
Sizing the bearings
Speaking of tolerances, it's up to and not your machine shop to determine what size crank and rod bearings you ought to be using. Your crank's journals don't ride directly on your block's main bearings or rod bearings. Instead, there's a fine film of oil that separates the two-a gap that you should be particularly concerned about if you want your engine to last. Use the appropriate micrometers if you've got them or Plastigauge to determine how thick or thin those bearings need to be in accordance with your engine's service manual.
Leave a rod bolt loose and you already know the sort of catastrophe that'll take place. What you don't know is just how bad over-tightening one can be. Which is exactly why you need a properly calibrated torque wrench and the appropriate torque specs for your engine, and which you're better off sourcing from a factory service manual as opposed to titeVTAKboy69 from the message boards. Lubricating fasteners with a few drops of assembly lube will ensure proper torque.