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My 5 speed was about the same way. I adjusted the clutch PEDAL under the dash and now it shifts smooooth!

New fluid can help too.

Id try adjusting the pedal to give it more throw. Adjust it as far out as you can and go from there.

How do you get to that adjuster bolt without removing the dash?

89 4Runner
3" BL, M/T locks, 33"bfg mt, bilstein, Kayline, tubebumper, toyotafiberglass panels
TBI: Elocker,3.4 w/ORS,b+b,S2Sstg2cams,arias pistons,P+P intake,TRDs/c,URDpullies+7th,downey headers,MAPECU2,WEGO WB, SupraMAF,walboro255,stg4clutch, EPaOo2 sim