For the 500- The 2 coils operate 1-4 and 2-3 respectively. Both plugs fire each revolution but only one is starting it's power stroke. Since the problems are on 1-3 it is most likely a carburetion issue with clogged jets. Pull the plugs and look at them. They tell quite a story about what is or isn't going on in the combustion chamber. Usually if they are wet and smell of gas, then it's an ignition issue (maybe a fouled plug) if they are dry and not firing then it's a fuel issue. Of course other things can cause problems, too. But, that's usually where I start with an unknown bike.
You'll find that the frames between the 500 and 550 to be different enough that parts swapping will be quite spotty. I think the rear wheel might go okay, I'm not certain, though. But, if it does, expect to move everything that's on the axle.
The exhaust systems will interface with each of the two engines. However, the mount locations for the mufflers will be different. If your aftermarket mounts aren't adjustable you'll have to make some adaptations. Neither of the 4-1s have the same flow characteristics as the stock exhaust systems (which were also different from each other between the two bikes) If jetting wasn't addressed when the replacement exhaust was installed you may have some performance issues. A friend of mine has a CB550K 77, I think, with a Kerker. And, he can't get it to sustain 80 MPH. It runs okay below that and he has other bikes. So, he just ignores the problem and just uses it around town. The 77 and 78 had carbs different from the earlier models and I think they were all tuned toward the lean side. Other issues include possible carbon fouling of the plugs and flat spots in certain throttle positions.
FYI, the K models were stock with 4 into 4 pipes. The F model cb550s were only made from 75-77. They had 4 into 1 and carbs jetted and tuned for that configuration.
As for parts missing from the bike... If you can't find these at local breakers, eBay will have it if you're patient.
Any CB550 tach from 74 to 78 will work on your bike. The printing style and colors of the dials will not be period correct unless you get one from a 77 of 78 model. Don't try a CB750 tach, as it will not read correctly due to different gearing even though they look the same.
The starter push button switch disintegrates when a leaking master cylinder bathes it in brake fluid. Any switch from an SOHC4 from 69 to 78 will work in your housing, I'm pretty sure. The stock switch interupts the headlight during start so it is somewhat unique for fit and function.
Good luck with your bike's resurection!
