What engine is this? I see one response suggesting it is a CB750 - is that what you're contempating?
Here are my suggestions -
1) Go to MR Cycles and print you a parts fiche for your bike and engine. These are extremely valuable for logging records of new parts needed and received - that way during assembly you can be sure to use all new parts that you've accumulated.
http://www.mrcycles.com/fiche_select.asp?vcc=Motorcycles&mfg=Honda#SDOWN2) Loosen the head nuts in the reverse order shown in the shop manual. Turn each a little at a time until all pressure is removed - Do not loosen and remove the nuts full one at the time. That torque sequence is there for a reason.
3) Get ZipLoc bags - quarts and gallons. Put "group" parts together logically. It makes finding them later and knowing what and where each goes.
4) Do not mix the cam towers and parts. They are lettered and have a specific place they fit. A sharpie is a good thing. Remember #1 is the cylinder on your left as you sit on the bike. #4 is of course on your far right. Use those ZipLocs to keep them "matched" up. That Sharpie will write on them perfectly.
5) Do not mix rod bearings. Take each rod assembly apart one at a time!!! The upper and lower fit only one way, but you do not want to mix the bearings for any rod. You may re-use them and you'll need to order replacements based on their size. No- all throws and all bearings are not the same size. The factory would have different sizes from the factory. Some, not all.
6) Do not mix the main bearings - again the factory used difference size bearings during machining and assembly - it's perfectly normal to have 2 even 3 sizes on a new motor. If you're careful and will mark your ZipLocs accordingly, this is as easy as tieing your shoes. It's likely one of things some un-skilled mechanics will over-look.
Remember, you're cases will be upside-down during this step - with the oil filter boss away from you - # 4 will now be on your left. The crank has 5 main bearings - same principal -#1 is to the left when sitting on the bike- turn the motor upside-down it's on your right.
7) Do not attempt to remove the cylinder studs. The cases need to be heated to expand the aluminum before you try to twist these out. Also, removal is "not" normal and not covered in the manual - simply because they should be left in-place and considered "not servicable". People will tell you they've done it, but 1 in 30 attempts will result in a broken stud. These are extremely hard and you will not be able to remove them by drill or easy-out. If you want to upgrade Jay's APE studs, then heat removal steps can be explained.
By looking at the manual, looking at the parts fiche, using slow and logical "grouping" technique with the ZipLocs, and take the time and care to label each, take photos, and notes for later, and the help from many of who've done this - you're going to be fine.
If you don't have a torque wrench - now is the time to get one. Several fasteners need the proper torque. Those crankcase nuts holding the mains, the rod bolts, the many 6mm nuts and bolts through-out, the 8mm cap nuts on the cylinderhead, ect - do not try these without a good wrench. Since you'll need 20 feet pounds on some and 80 inch pounds on others, I suggest the Craftsman Microtorque which is good for 15 "inch pounds" to 250 "inch pounds" (you get feet pounds simply by dividing the those inches by 12) - that wrench will easily handle the 80 inch pounds of almost every single 6mm nut, bolt, and phillips screw on the bike and engine. Most 8mm nuts like the 168 inch pounds, while the two cam 7mm bolts need Blue Loctite and 105 inch pounds.
See, it's easy when you take your time. The investment in a few tools will last you forever.
Regards,
Gordon