I’ve got a 2000 4x4 v6 manual. 2nd gear has always had a grind to it especially once it warms up. I’ve changed slave and masters, clutch fluid, marlin heavy duty shifter seat, red line mt90. Now I’m about to change the clutch out but I’m considering ordering a marlin crawler rebuild since the transmission will already be our. Should I swap the clutch, throw out, pilot, clutch fork and whatever I can get to only or go ahead with the marlin tranny?
Sounds like your syncro is shot. Common wear symptom, and you did everything possible to remedy it with out pulling it apart. Just needs a rebuild. In the mean time If you make a slower concentrated meshing effort on on the 2nd gear shift you can eliminate the grind while you drive it. You may have chewed up that gear, but you'll find out what it looks like when its torn apart.
Here's a pic of mine apart, so you get an idea on the gears.
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*1999 3.4L, 4wd/5spd, swapped motor and trans, heavy use DD, seasonal rust proofing using WD-40 only
*2000 3.4L, 4wd/5spd, parts rig, picking the carcass