Please note: This will be a long "work in progress".
Photos and specific details will be added to every procedure.

Crankshaft assembly

• Check connecting rod for correct clearance (both ends)
• Size connecting rod if necessary (either/both ends)
• Check connecting rod for straightness (fix if required)
• Polish ends of crankpin and edges of crankpin bores in crank halves
• 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 above)
• Check case for "square" (top of case parallel to crank centerline)
• Square bottom of case (4 "pads" that sit on motor mount) if necessary
• 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, 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
• Disassemble, trim piston, reassemble for 2nd check - if all OK, proceed

Piston/ring

• Deburr and clean piston
• 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