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We have a lot of TRX500's sold and none back yet with this type of transmission trouble .. I've had several 500's tore down for crankshafts (part of the clutch plate recall) .. Honda used a different type of "gear dog & slot" on the 500 .. I'm not a big fan of this type of transmission ..
This is the dog & slot style on most older & some new Hondas the slot holes go all the way thru the gear and seems like a more positive lock when it's in gear....

This is the TRX500 type dog & slot .. As you can see the slot holes don't go all the way thru the gear ..

Was your transmission gears ,shafts & shift forks measured before re-assembly ..The shift fork that goes with the gears that were replaced must have been replaced also I hope .. And I hope it was assembled using the shop manual to make sure the thrust washers were the right ones & in the right places ..Over the years we've even had a few transmissions apart that Honda assembled the thrust washers wrong or had thrust washers missing..
Here's a picture of the mainshaft & a picture of the countershaft from a TRX500 .. Everytime the transmission gears are off any circlips removed should be replaced with new ones and the sharp edge of the circlip should face away from the side with pressure against it..


This is the dog & slot style on most older & some new Hondas the slot holes go all the way thru the gear and seems like a more positive lock when it's in gear....

This is the TRX500 type dog & slot .. As you can see the slot holes don't go all the way thru the gear ..

Was your transmission gears ,shafts & shift forks measured before re-assembly ..The shift fork that goes with the gears that were replaced must have been replaced also I hope .. And I hope it was assembled using the shop manual to make sure the thrust washers were the right ones & in the right places ..Over the years we've even had a few transmissions apart that Honda assembled the thrust washers wrong or had thrust washers missing..
Here's a picture of the mainshaft & a picture of the countershaft from a TRX500 .. Everytime the transmission gears are off any circlips removed should be replaced with new ones and the sharp edge of the circlip should face away from the side with pressure against it..

