You can use an OEM waterbox without issues. Some high torque starter like the Gokis you will want to stay away from as they are not durable and fail often. Aqua Torque makes a good HT starter, however an OEM should be more than adequate for any 550 motor, even one with raised compression.
You can used the 650 carb, however you may need a manifold (most 650s had Keihin carbs and were either 28 or 38mm, where as the 85 550 had a 38mm Mikuni). You will aslo need to dial in that carb, it will not just bolt and go.
I have motor mounts, hardware, and an OEM starter if you are stil on the hunt.
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