Recently bought from Japan Yahoo auction as the item stated as pgm3(mc21) gearbox dryclutch as im going to put it into my mc28 but later i found both are the same gearing number. Can anyone possible help me what or where can i spot the different of both gearbox..

As far as I'm aware, the gearbox is the same, just the primary gears are different between models.

So your need to remove the small primary gear attached to the MC28's crank (not an easy task!) and replace with an MC21 one.

If you look on the site you can find the specs that show the different ratios between the 2 boxes , 4,5 & 6 are different on the 28 model .
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NSR300

The primary engages with the gear on the back of the clutch basket, Tom. It's irrelevant which transmission is being used.

The MC21 and MC28 have different ratios for the top 3 gears. The MC21 is geared lower, I seem to recall.
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Andy.
NSR-WORLD.COM

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Neal beat me to it!

You can mix'n'match primary gears, so long as you use the corresponding clutch gear too. So, if all you are changing is the transmission, there's no need to use an MC21 primary.

MC21 6th is 1.083 (24/26), and MC28 is 1.00 (25/25).

You can see the differences between the MC21 and MC28 here: NSR250 Specifications.
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Andy.
NSR-WORLD.COM

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I have counted amd both have 25th teeth on the fifth gear if im not mistaken..

Gearbox in and now doing the rs coil..