There seems to be a bunch of folks on here that race RD's so I figured it was worth an ask. Just got my long project RD running last week, motor was assembled by me 3yrs ago and sat with oil in it until last week. I got the bike together doing some carb tuning around the neighborhood and it ran fine no noise. But first time I really got it opened up above 80mph the trans started making noise, opened it up and saw 2nd gear was discolored and gauled the heck out of the axle shaft, 6th gear across from it was also starting to go. Oil was full drained 24oz pluss what I spilled , pretty hot porting 50+HP, Trans was all NOS parts at rebuild. So is this shit luck or am I missing something that caused it..
Well upon further inspection, it looks like the clip next to 2nd gear lost it's ends somehow and I assume caused the failure..... oh well shit luck it is I guess.
Although you have solved your problem, I think one minor comment may be in order: you said you drained out 24 oz of transmission oil. All RDs say on the clutch cover that they take 1500 cc of transmission oil, or a quart and a half, or 48 oz, double what you had. RD transmissions do not like running on less than full of oil, the gears can seize on the shafts if you do. FWIW
I just rebuilt my entire RD350 motor last year. I thought about reusing the clips in the trans but figured if I had it apart replace them. So I did... The trans had a bad bearing and it scarred the shaft a bit. I sanded the shaft down with some 1200 grit and it measured and cleaned up fine so I put it back together. Been good so far and I've ridden the shit out of the bike all year. I like the little ring ring ding ding dingers