If the pilot bushing is worn it would cause more clutch engagement issues when the engine is running. If the bushing got damaged during removal of the trans or when it was installed it will cause your problem. If the trans was removed without any weight put on that bushing (i.e. it didn't hang at all due to improper removal equipment, or the trans was not forced at all into position during install) then the bushing should be okay. The pilot bushing must always be replaced because its only protection is a small amount of grease that can never be replaced during its life (plus it's really cheap).
Next, if the wrong grease was used or too much, that could cause the trans output shaft to spin when the turning flywheel with clutch depressed. You can check this by turning flywheel with clutch depressed and holding output shaft of trans. I would change out bushing, use correct grease and correct amount and ensure proper install procedure of trans so as to not cause damage of bushing during install. If you can stop it then it could be bushing or other clutch parts not mating properly or working together. If you cannot hold the output shaft from spinning I would suspect incorrect amount of travel for the csc or a worn csc shaft (tube that csc slides on) which should be replaced when doing clutch. Hope that helps a bit.
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