My son just recently ran his '02 XR200 out of oil so we tried different parts from different years.
Off hand, the jug from the '02, from an '83 or '84 trike and from an '83 XR all have a different bore.
The trike had a dished piston.
The jug from the '83 XR didn't have the hole drilled through for the long bolt that goes through the head down to the cases (just outside the timing chain)
All 3 heads looked the same. I didn't find any difference there.
The jounals on the crank of the '83 were smaller than the ones from the '02.
So even though they may look the same at a glance things did change over the years.
Good job on comparing parts.
To my knowledge all of the XR/ATC heads flow basically the same with some variations that seem to be foundry related, so for a trail bike any of the XR/XL/ATC/185/200 heads should be OK (the TLR has smaller valves). All 79-02 XR185/200 cams are the same, all of the other model cams are milder. To be on the safe side use XR valve springs with the XR cam (or do some part number searches on valve springs).
The bolt is a 6x116mm and used on all of the common large 2 valve motors including the 83 XR200R, so the head you have must be from something different. I have several ATC heads and they all have the bolt hole.
The nominal displacement of the engines is cast into the rear of the cylinder, I use that to ID cylinders but the bore size differences among the XR/ATC/XL/TLR/185/200 are just that, the liners have the same OD so you can rebore to suit your needs, but some machine shops charge more if they need to bore out more than one oversize. Stock bore for all of the XR200s is 65.5mm, ATC200s are 65mm and XR185s are 63mm. I've bored a 63mm XR185 cylinder to 66mm for use on a XR200R. The clue is they all use the same base gasket. The XRs use a 10:1 piston. Once upon a time Honda use to list oversize pistons in increments smaller than 0.5mm but it seems cheaper and easier to use 3rd party forged pistons in 0.5mm increments, rather than Honda cast pistons. Although for trail riding I doubt if it makes any difference in engine life.
The only difference in crank journals that are obvious between early/late XL/XRs should be the timing chain sprocket, in 90 the crank sprocket ID changed to 22mm ID from 20mm. Most of the ATC cranks have a long right shaft for an auto clutch so they won't work. The XL/XR bearing journals should be the same except for a change in fit for the right side that occurred in 94, so right crank/bearing/case need to be compatible.
There were also some differences in the left end taper on other 2 valve motors to suit different rotors, but the XR185/200 left cranks seem to be the same. I've mixed early/late rotors and cranks, rotor bolt needs to match the rotor. The 86+ rotor is 12 oz heavier than the early rotors, but you also need the stator/cover and electrics.
To the OP; IMO the 86+ Service manual is better because my 81-83 XR200R manual has some bad torque values for the engine, my 86-99 Honda manual is correct! Any 79-84 XR185/200 or 81-83 XR200R motor will just bolt into your chassis, just use your electrics and carb. Even a XL motor will fit but it will have less compression, only five speeds, and a milder cam, but you can run street lights.