I don't have a comprehensive guide, but am in the middle of my second rebuild. Seems that if you take it in pieces, its much easier. My current rebuild is a frame-off, and I've lost track of where some parts go (oops). Here's a tick list of what I've done on both:
Degrease engine/frame
Remove all chrome and steel wool/brush, and polish, replace if necessary
Clean/rebuild carbs
Disassemble fork tubes, replace seals (tubes if necessary)
Replace steering bearing with tapered bearing
True front wheel, check/replace bearings and seals
Check front brakes
Fully disassemble/clean/check/lube right and left hand control switch assemblies
Check all wiring connections in headlight bucket, repair if necessary
Replace sealed beam with reflector type headlamp
Reassemble front end, torque everything to specs
Check all wiring connections in rear, repair if necessary
Pull rear wheel, chain, swingarm, replace with new needle bearing swingarm pin
Check rear shocks for leaks, replace if necessary, or just clean and polish chrome
Check chain and sprockets for wear, replace if necessary, or clean in kerosene
Check/replace rear wheel bearings and seals, true wheel
Check/replace rubber cushions inside of rear wheel assembly
Check/replace rear brake pads/shoes and check rotor/drum
Reassemble rear end, tension chain,
Remove all cables, check/lubricate all cables, replace if necessary
If gauges are ugly, disassemble them, clean, paint, give them decals
Check all light bulbs, test for proper operation (indicator, instrument, etc)
Remove and clean coils and spark plug cables, replace with Dyna coils if necessary
Check all spark plug ends for proper resistance
Check/gap/replace all spark plugs, points, and condensors
Use POR-15 kit to clean and coat gas tank (MUCH better than Kreem kits, plus its silver)
Drain oil from engine, remove oil pan, clean out metal shavings from the pan and oil pump screen
remove/replace exhaust, reinstall with new exhaust gaskets
Replace oil filter, put in fresh oil
Adjust/bleed brakes
Double check torque on all bolts
Fill 'er up, and start it up. Probably will run very rough, s do your best to adjust the carbs. At this point, I take mine to a local shop that balances the carbs for $35. Very reasonable.
Bottom line "expect to replace" parts seem to be:
Wheel bearings (front and rear)
Bearing seals (front and rear)
Outer engine seals (kickstart, shifter, drive shaft)
Fork seals/boots
Exhaust gaskets
