Please note: This will be a long "work in progress".
Photos and specific details may eventually be added to many of these procedures, if there is enough interest.

Please note that while this is written somewhat specifically for the Yamaha KT100, the exact same principles apply to most any 2-stroke (and conceptually even to 4-strokes)

Crankshaft assembly

• Check connecting rod for correct clearance (both ends)
• Size connecting rod if necessary (either/both ends)
• Check connecting rod for straightness in both axis (fix if required)
• Polish ends of crankpin and edges of crankpin bores in crank halves (more important than it seems)
• Possibly install "crank savers", requiring 6205 bearing (stock is 6304)
• Clean everything as if it were going on the Space Shuttle
• Assemble crank to correct width (determined in next section) and align

Crankcase assembly

• Clean/lap center (sealing) face of case halves
• Check bearing interference
• Check bearing alignment
• Check "roundness" of bearing bores
• Fix one or more of the above if necessary/desired
• Install main bearings (something other than stock, most likely)
• Assemble case halves, and measure distance between bearings (measurement used to set crank width)
• Check case for "square" (top of case parallel to crank centerline)
• Square bottom mounting surface of case parallel to crank centerline (flatness of this surface is most important)
• Square top of case to crank centerline if necessary (could be done before or after bearings installed, depending on method)
• Reinstall studs in top of case
• Clean everything as if it were going on the Space Shuttle
• Install seals
• Disassemble case, and reassemble with crankshaft
• Double-check crankshaft endplay now that lower end is assembled

Cylinder

• Overbore if you're convinced you need all displacement you can get
  
• Possible "porting" of intake and exhaust port, remember: cast iron at bore/port interface must remain untouched on a KT100
• Hone cylinder to correct piston/cylinder clearance, preferably using "torque plates" (exhaust header and "dummy" cylinder head most important)
• Square bottom of cylinder to bore centerline (some might do this before finish hone)
• Machine head gasket recess square to bore centerline (debateable if necessary)

Test assemble for measuring

• Install piston on con-rod (no ring)
• Install cylinder on lower end using any base gasket and torque to spec (150 in/lbs is what I use)
• Use a dial indicator to check how low the intake port opens, and how high the exhaust port opens
• Calculate what is required for base gasket to set exhaust port where you want it
• Calculate how much trimming on piston skirt to set intake port where you want it - don't forget that base gasket change for exhaust effects intake opening
• Disassemble, trim piston, reassemble for 2nd check - if all OK, proceed

Piston/ring

• Deburr and clean piston
• Check piston for square (another article on this web site explains how)
• Check/set ring endgap, lap ring, and check (light check) fit in cylinder
• Clean everything as if it were going on the Space Shuttle

Cylinder head

• During test assemble (above), torque down cylinder head and check cc's and squish clearance
• Cut cylinder head to obtain desired shape, cc's and squish clearance/angle

Final assembly

• Clean everything (again) as if it were going on the Space Shuttle
• Assemble upper end (piston, ring, cylinder & cylinder head)
• Double check port timing and cc's if desired
• Install ignition and set coil clearance

Carb

• Drill any holes you feel you want close to maximum (use care!)
• Clean everything as if it were going on the Space Shuttle
• Assemble carb using arm height and pop-off pressure settings you desire
• Install carb

Some/many of these items could be done in different order.

More could be done that I have not mentioned (i.e. bore carb venturi to max, bore intake manifold to max, shorten intake tract length to minimum, etc. etc.). This is only a brief list of the items that quickly come to mind.

Many of the "settings" should/could be personal preference (or the preference of your engine builder): port heights, combustion chamber shape, cc's, carb hole sizes and carb settings, etc.

Pete