Well where to start is to completely disassemble it. These engines are pretty simple, and if you re-install nuts and bolts into their holes and studs as you take bits off, the hardware will prettymuch take care of itself. The house starts with the foundation, so after it is completely apart, I would reccomend starting at the bottom and working up. Flip the main casting upside down and start by leveling, and placing the 4 feet onto the same plane. The feet on mine were not that great, and I spent a fair bit of time with a file guide bar I made, getting the resting surface of the feet so i could sight across all four surfaces from any other surface. This is fairly easy with a guide bar. This thing needs to be bolted down tight. If you attempt to bolt down to a flat base with uneven feet, you will be placing stresses into a cast iron case that really shouldn't be there.
Next is the case interior. Not being painted is good, as it should be clean of sand, and you can easilly check this. Lots of places inside that are hard to see even when stripped down, let your bare fingers do the walking... You will probably want to paint it yourself as the cast iron is porus, and a layer of paint inside after it is cleaned and inspected will help to keep the oil inside:)
Next I would work on the deck. The deck is the top of the case where the head studs go and the cylinder rests. You may have noticed when you took the engine apart that you had half gaskets under the base of the cylinder toward one flywheel or the other. These gaskets are to get the cylinder bore perpendicular to the crankshaft. The reason this dosn't happen naturally, is the case holes where the crankshaft bearing carriers go are not machined parallel to the deck. This may be due to uneven feet on the case:) and the fact it is a dam big and heavy casting to position accurately... Half gaskets are acceptable, but if you have the tools and the talent you can modify the case and rollerbearing carriers to be parallel with the deck, then a single gasket can be used. The one tool you should probably have is a machinest precision level. This and some inginuity and you can walk thru measuring parts to check for proper alignment fairly easilly. You continue to work your way up with cylinder and liner checking for perpendicular and square, with the final adjustments being made with half gaskets as necessary and using differential squish as a measuring tool.
I did a complete writeup once upon a long time ago, I will try and find it and I can E-mail it to you if you wish... I would say as you start with these things, start posting questions here. It is going to be a bit of work, but it is SO COOL when it puffs for the first time after you crank it up to speed:)
Good luck.
Ron