Popping out of gear IS one of the early signs of transmission failure. The gears are held in by the design of the synchros. The synchros have little teeth around the outside of them. When engaged in gear those teeth lock into one another due to the opposing taper of the teeth on the synchro ring and the gear. As the teeth on the synchro and gear round off due to normal use and abuse over time they lose their positive lock due to the edges of the tapers rounding off. Once it gets rounded off too much it'll start to pop out of gear. Your tranny needs a rebuild. It is simply a coincidence that you're only noticing it after the clutch job. I'm willing to bet that you knew the clutch was weak before and you drove the car easier to protect it. Now, with the new clutch, you're likely driving it harder and now this issue is appearing. The issue was probably present before, you just didn't notice it. Maybe because you drove it easier, maybe because the new clutch grabs harder.
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