On the old Zephyr-Zone site before it got relaunched and lost every bit of content, there were a couple of threads of guys putting the zx600 motors in their 550's.
I really really wanted to do this, but I ended up finding a spare 3K mile motor, so that ended the need to do the swap.
These are some of the issues that I remember from doing the swap, but being for a zr550, some concerns may not apply to the gpz550.
Although the zr550 engine case is identical to the kz550, so fitment issues do apply.
The front rubber isolated motor mounts just had to be swapped side-to-side to accommodate the zx600 motor. The gpz still used solid mounts in 81 so that bit of info probably dosen't apply.
The bottom rear motor mount lined right up, but the top rear mount spacing is narrower on the zx600 case, so new spacers had to be fabricated to mate up with the gpz mounts.
The zx600 has a longer output shaft on the transmission (10mm?), so an offset sprocket may be needed and then installed backwards in order to line up with the stock gpz rear wheel setup.
In the UK, most versions of the zx600 did not come with oil coolers, so guys who were swapping in motors that did, had to find oil sumps without the oil cooler ports, as there was little room for the radiator, exhaust header and an oil cooler. There wasn't ample room for all of it without the risk of the front wheel coming up and possibly crushing the oil cooler during a hard bump or the exhaust heating up the cooler itself. But possibly the oil cooler could be remotely mounted under the battery tray as others on here have done.
There was also little room for a fan on the front of the radiator, so they never ran with one or they fitted a massive radiator for maximum surface area. But in the UK the weather is predominantly cooler so they could get way with it.
Finding room for the expansion tank, piping that allows for air removal and getting a fan to fit on the radiator will be the most challenging issue to solve.
Ignition box and a pulse pickups on the zr550 worked just fine with the zx600 as the ignition curves are almost identical. The stock gpz mechanical advance will probably bolt right up with no modifications and will most likely work, but never give proper or full performance. And performance is the real reason for the swap is it not?
Factory pro makes a jet kit especially for the zx600 motors to be used with pod filters as the cvk32's won't mate up with the gpz airbox very easily or at all.
The gpz exhaust will bolt right up to the zx600 motor. No modifications needed.
Food for thought....