all XR600 are 591cc 97X80 bore\stroke; early model 85 - 87 is twin carb equipped, 88 - 00 are single carb.
design of the heads are different between these 2 versions: the later (single carb) has automatic (centrifugal) decompression system (it's mounted on the camshaft right side), so camshaft are different (non interchangeable); the camchain and its wheels are narrower in the single carb motor (to have room for the decompression device).
except the heads, the motors are identical, except for the covers: magnesium (super lite and brittle) for the early 2 carb motors, solid , heavier alloy for the single carb motors (anyway they are interchangeable)
note that the XL600R motor (83 - 87, twincarb) are very similar, but they are 100X75; many parts are interchangeable with the XR motors; actually the XL600R it's a larger bore XR500 (83 - 84) motor
all these motors are bulletproof, if you care to provide them frequent oil changes: only the stator failure (they become fried often) can stop them