Did the tcase sit properly flush up against the trans or did you ha e to tighten it down to get it to contact?
Known good combo?
Did you put a new clutch/throw out/slave/pilot in with the new motor?
What oil?
With the tcase in gear the input is not spinning which means the clutch and syncros are doing all the work. With it in neutral the tail shaft and input at spinning with the main so it easier for them to line up.
Either something is binding or the clutch isnt fully releasing.
Known good combo?
Did you put a new clutch/throw out/slave/pilot in with the new motor?
What oil?
With the tcase in gear the input is not spinning which means the clutch and syncros are doing all the work. With it in neutral the tail shaft and input at spinning with the main so it easier for them to line up.
Either something is binding or the clutch isnt fully releasing.