You can drop a bottom end of a 650 in a 550 case and lose your kicker, but the 650 deep oil pickup requires a modification to the oil pump pickup when in a 550 case. Was it FunJimmy or Brent Waller that documented that modification, I think it was Brent. He blending the oil pickup of a 550 with a 650 with some TIG work...and lots of measuring. Don't recall if he used the deeper oil pan of the 650 and thus the needed mod. But, then again...Brent has a custom solution close ratio 6 speed gearbox in his 550 race bike...initially putting it together with 350 or 360 six speed parts. Later with some custom cut gears after a couple gears broke teeth. If you want to see a Potent 550 motor build, read Brent's thread in the High Perf section... Really sweet race bike and high 70s hp now... Or is it 80?
The 650 crank gives you long throw (or a stroker) setup. Like others have previously said, LOTS of engineering Paulage put into building his Hybrids. Too bad he isn't around to fill in some blanks in his thread and answer a few questions. He would really be bugged a lot I'm afraid as it is a cool topic and build. But as SOHC4 Cafe Racer Fan has said, going with a 650 motor with an overbore is a better route to up-rating the 550 chassis. Just a stock rebuild gives you a much nicer power band, if you defeat the CDI ignition system shortcomings, easily done now with a cash injection.
But, you are also going to spend some money with Mike (MRieck) to get the modifications to the head for running a high performance camshaft with that 650 head. He has it figured out now, but as he said it took him a while to figure it out. His head work is worth every penny, a TRUE ARTIST when it comes to tapping into power for any of the SOHC4 heads.
Would love to give him a pair of CX500 heads to see what magic he can do with them, but cam choices are highly limited to non-existent for the CX/GL500 bikes. It is far less expensive to be happy with the stock performance or mild upgrade with the SOHC4 and similar vintage bikes. Later bikes or more modern ones have far better performance easily, without the shortcomings of the brakes, chassis flex, suspension, etc. You can spend $10K on a 70s SOHC4 and a 80s or early 90s DOHC of similar displacement will outperform it very easily in power and handling. The classic styling you can't get though, at least in a Honda as even the "standard" bikes of the 80s took on a different look than the lovely lines (in my eyes) of many of the 70s SOHC bikes.