Updated the cosmetic/nice-to-have part of the spread sheet. This is factored into it's own total. I don't have all the nuts and bolts as I'm not sitting in front of the bike currently. But, let's assume ~$100 each for the larger parts such as the headers, exhaust collector, fenders, etc. for any eBay/Forum Wanted sales. Add the paint work in, with me slipping one of the old body shops I worked at a $50... Easily $1500-$2000. I will not be doing any of that this year, except some small pieces here and there if I have some extra money/time. After this rebuild I want to focus on an engine rebuild of the CB550K and then I will return to any cosmetic stuff after both bikes are mechanically sound. There is zero point on looking flashy if the engine health is mediocre/bad in my opinion. Get that engine correct first, ride it around with new consumables, put a couple of oil change intervals on it and do the fine tuning. Make sure it's perfect before you worry about how it looks.
With that said... what does it take to do a complete rebuild, parts replacement of consumables (chain, tires, grommets, bushings, etc.) and obsessively replacing nuts and bolts that the world can see when parked, and respray of a 400 Twin? I'd say about $4000-$5000. This includes shipping, and you getting screwed on some pieces that take a while to find and you have no choice but to pay a ridiculous price. Add more if you plan on doing a seat cover, lens replacement, painting the frame (won't be doing this). Then you're getting into $5500-$6000 territory. Add a few hundred more if you want to replace/restore bouncy speedos and tachs. Add another $60 for a battery.
If you want to go all out nuts factor in a CDI, stator rewind, completely redoing the harness by hand with the proper colours connectors, new ignition coil with wires and caps, bulbs... Add another $800-$1000. Now you're looking at $7000. Maybe a bit more if you feel you must replace the turn signal relay and rec/reg and solenoid. Now closer to $7200-$7300. So let's be nice, add some realistic fudge room and just round up for all the shipping costs... $8000.
Could even cost more than that if you need to find a good engine because your crank and cam shafts are shot. Add even more if you get the carbs rebuilt professionally. More if you send the entire bike to a professional. Now we're looking at $10,000... maybe more. Let's be fair, say $11,000-$12,000 so you're not surprised when the keys are handed to you.
This sounds like a lot, but it's still cheaper than buying a lot of new bikes out there.
Is it worth it? To me, yes. I like this bike a lot. Been through a lot of adventures with it. I know I will NEVER get back what I put into it. These bikes are not investment. Antique car guys learned the hard way when putting $20-$50K into their cars and got upset that nobody would pay $90K or even $30K.
You can easily buy one in great condition for about ~$2000, and then factor in a total engine rebuild, including new insulator and air box bands, insulator o-rings, and the rubber pieces of the carb... you're looking at about $4000-$5000 total. You can save and cut corners if you're simply doing a top end.
PS: This assumes OEM parts. No sense in going all out and then getting aftermarket. Exceptions to this would be the ignition coil (unless you really must have NOS), spark wires and caps, air cut off valves and fuel accelerator pump, carb passage plugs, chain, sprockets, tires and tubes. If you insist on finding an NOS ignition coil, CDI (highly recommend you don't do this as capacitors are "use it or lose it" just like a battery), stator/rotor, air cut off valves, fuel accelerator pump, buying the carb rebuild kits NOS to get the Honda passage plugs, somehow source an original NOS rear sprocket (good luck) then all bets are off. I'd say now $14,000-$15,000 if you can find this stuff.