Man, a lot of 650 swaps coming up!
Benefits of the earlier years (79/80) is that early 750 carbs fit the head spacing. That really only matters if you don’t have carbs or they’re not in good shape. I believe the early 750 carbs are easier to come by. I also have heard that CV carbs are not easy to tune with pods.
The later years were styled like more of a cruiser. The frame on those are more swooping, if that makes sense. The early years were really just an upgrade to the 550. So they were styled similarly.
There are internal differences in the later years vs earlier years of the 650 but only in gear ratios. Primary reduction, all gears and final drive were different. The later years were slightly geared for highway “cruiser” type gearing where the earlier years were similar to the 550. That doesn’t really matter though. Minor differences. Plus, you can drastically change the way the bike feels by changing out sprockets.
I do not have the original air box, the 650 air box won’t fit in the 550 anyway even if you wanted to use it. I have CR26 Special carbs and they’ve been dyno tuned. Runs fantastically.
Another possible issue is that the petcock on the 550 (at least on my ‘78 550k tank) hit the CR carbs. I had to move the petcock rearward about 3-4 inches. The valve cover on the 650 is shaped differently so it comes close to the petcock. It depends what carbs you have whether or not it will be a problem. You can see in the picture where the petcock used to be, circled in red. You can see how close it is to the motor.

Oh, and lastly the exhaust for the 650 probably won’t fit on the 550 frame. I haven’t confirmed this because the exhaust for my 650 donor had to be trashed. I got the Hindle exhaust from Ripple Rock Racers. This would be nice for someone to confirm! And no, the 550 exhaust can’t be used on the 650.
So all in all it’s not exactly a direct swap. But with some minor effort it will fit and it’s an amazing upgrade. Check out my build thread for more info. There’s a table of contents on the first page which makes it easier to find things.