Interesting. I see two blue u-cup seals on the bench. Where does the second one go? That would be the one for the rod end, but I agree, I don't see it going in the bore easily.
Pictures will not come up due to permissions. Can you just attach to your post? Also, your description is unclear as I read it the same way as @John0829
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If you look at the parts book, the oring for the 3000 measures 2.825" (0.215" thickness + 2.61" inside diameter), so it can't be 3". The only place the roughness of the piston would cause problems is around the oring groove. You can clean the old one up and take the sharp edge...
Probably dealer gets a better bulk buy from NH on oil. JD does have different recommendations for some of their industrial stuff. JD excavators call for JD hydraulic oil while Hitachi excavators, which make larger JD excavators spec'ed their oil only!
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The 1210 will run a 48" flail just fine.
Many to look at, but here is one that is just a flail mower:
https://valleytoolmfg.com/vrisimo/minimax-flail-mower/
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Hard to tell whether you would need to split or not, but my guess is, being a prison unit, the shifter was forced and something like a fork is bent. Not a terrible repair.
I resealed/rebuilt a 4500 not ling ago that yses the same system. I can't remember how I got the tapered pin out, but it was something similar, just minus the air hammer. The leaks are the easy part. Fixing the play in the linkage could get expensive. I has one part machined to replace a worn...