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RG500 Specs:
498cc
2 Stroke Sq. Four
406 lbs Wet
4.5/1.3 Gal Tank
279/72 Kms Range
6 Speed Tranny
Rotary Valves
28mm Flat Mikunis
7.0-1 Compression
96 Horsepower
110/90 16 F Tire
120/90 17 R Tire
56.1"  Wheelbase
25.2 Degree Rake
31.3" Seat Height
5.8" Clearance
0-60 in 3.04 sec
1/4 M in 11.37 sec
Braking 60-0 111ft
 
 

1) Carb slide needle and main jetting: 400 = #135 , 500 = #120
Keep your 400 needles and jetting, it's better (any other comment here may be entered).

I believe the 135 jets are the restriction on the 400.I know Paul Lewis went as lean as 100's and found a great difference.  I think he altered the needle height too though (you reading this Paul?)  Someone also told me they find the 400 needles to be a bit crisper at lower revs so it might be best to keep them.  (Added by Kevin Wooldrage)

 
2) Clutch: the 400 has some friction disks less (1 or 2, I'm not sure). See if your clutch will work OK so you may leave it as it is (comment?).
 
3) External sprockets and chain, 400 = 15 front /41 rear, 525 chain, 500 = 16/40, 530.
You may go for a 520 sprocket/chain conversion.
 
4) 400 pipes have only thiner stingers, all the bodies are the same
 
5) Cylinder, piston: 400= 50mm 500=56mm
400 has 5 intake ports, 500 has 7 intake ports but smaller (but 400's port in total I think give better flow - i.e. less divided area)
External lower sleeve diameter 400=60mm , 500=66mm
You need to rebore the upper crankcase.
But I'm not sure if you can rebore your 400 cylinder sleeves to reach 56mm so you won't need any crankcase machining (and won't need to buy a 500 cylinder set). Remember the 400's cyls may give a better intake port flow.
 
7) Heads diameter accordingly are of: 400=50mm , 500=56mm
 
6) Conrods are the same, only its lower bearing consists of some more (1 or 2, I'm not sure) needles so they are closer each other. You may not bother splitting your cases and keep your 400's bearings though if you go arround the stock 500 horse power (no much more).
 
7) Some small difference in the front brake rotors. 400's are no "floating" type.
 
8) The rotary valves have different base, the 400's is thinner and lighter so keep your 400's (comments?).
 
I'm pretty sure your reference to 500s service manual would be OK (at points that don't have to interfere with the above differences).
 
Thanks to RiGas for this information :)