Manual transmission whine and popping out of 5th gear.

Recently had engine replaced, clutch replaced, etc. Now transmission has a whine and will not stay in gear on its own. It pops out of gear. I have to hold the stick in 5th gear to have 5th gear work. When you first start car whining is ver loud, after 10 minutes or so of driving noise almost completely disappears. If the clutch pedal is depressed the noise also almost disappears even when transmission is cold.

My question is: what could cause this whine and popping out of gear. I didn't have this problem before the engine was swapped. Same size engine was replaced. Could it be linkage, bad throw out bearing, or pilot bearing?