I have built some of the 'big bore' 500 and 550 engines, one with the Megacycle Cam 126-00. That one ran past the ton with less than 200 miles on the clock after the full rebuild, haven't kept track of it since then, though. Stock air intake tract, too, nice and quiet. I did a little porting to the head and intake manifold on most of them, more on the one with the Megacycle cam. This particular cam will last far longer than the cheap Webcams, too.
The pipes: until you pass 11,000 RPM you won't find any difference with any version of the pipes that improve exhaust suction that will fit: the bike is far too short to supply any 'header effect' from pipe length tuning or 4-1 'votex' setups. For one solid example, search for "CB750 Dunstall 4-2 pipes" to see the one version of pipes (with muffling) that actually have header suction, and you'll see they stick out almost 8" past the rear wheel on a 750 - this would be almost 16" on the 550 frame(!).
Watch the chamber volume with the 650 head. It is very easy to end up with a too-large chamber with these small-bore pistons, so I'd suggest that any use of the 650 head shuld be accompanied by the 590cc bores, too. Be DEAD SURE to make the piston clearance LESS than 0.0010" (0.0006" nominal, that's not a typo) and find a machine shop who WILL DO IT, or else find another one. When I lived in IL (1970s) I found it difficult (almost impossible) to get them to do it MY WAY, which was also HONDA's WAY, to make these bikes work right. If the piston clearance gets past 0.0014" then it will both burn and pump oil, everywhere, and in huge amounts above 8000 RPM.
Mill the cylinder deck by 0.010"-0.015", regardless of bore size. This will match the mated pair over the too-thick head gaskets that are 100% of the parts you wil find now: they are all 0.2mm (0.0008" thicker than in the 1970s, which means they will leak oil from the oil jets on the sides of the cylinders at the head joint unless this is done. You can alternately use thicker O-rings (or do both) over those ports to stop leaks, which I'm outlining even now in my upcoming CB500/550 book.
The intake ports are choked. A lot. In the 650 head, a little less, but still a lot. For hi-RPM use you will need to open those up. Smooth out the exhaust side, too, to reduce carbon buildup and head heating on the exhaust side at hi revs. The valve reliefs in the pistons (intake side) should be deepened at least 0.5mm to help ensure the pistons and valves don't move into each other's real estate at speed. If you can find (or make) a slotted cam sprocket, this will let you delay the intake opening slightly (2-5 degrees, depending on what you can put up with as loss of low-end torque in favor of more HP up high) to also help reduce this valve-piston overt friendliness.
The 550 carbs will work to about 10,000 RPM quite well, then they get uncontrollably rich (with pods) or lean (with OEM airbox setup). If you switch to 26mm carbs like from the CB750a, the pods will fight you every step of the way for tuning without blackened plugs, or having severe flat spots, so you will be faced with either trying to fit the pod filters into the frame (it is in the way), trying to create a way to use the 2-carb K&N style pods (with some sort of cover to block off the upper 2/3 of it) and fit those into the frame, or make your own: use a breather hole NO LOARGER than the opening in the venturi area at 80% throttle. There also needs to be more restriction on the 750-style carbs' intake side to generate an intermediate air pressure (lower than in the float bowls, higher than in the vebturi) to make them work, or they flat out will not work below 5000 RPM in the 550/650-size intake tract/valve due to low flow velocities. The intake valve size determines the carb size needed for peak power, so keep that in mind as you go.
A hint abuot startup after radical builds: retard the spark timing (I use 0 degrees TDC) for initial startup until you can feel your way into getting it to start and idle well. Then you can advance a little more until that is happy: also increase spring tension to retard the too-fast (in 1974) spark advance on these gadgets. I cut off at least 1/2 turn from both springs as a starting point in these engines, and it always works out well in use. If you use the AD125 (CB750K0/1/2) knock-off (new) spark advancer from 4into1.com, it comes with real strong springs (at least the last 2 I bought did) that are too strong for the 750, but might be pretty close for a big-bore 550 build.
