As far as gear stick, it can happen with any manual transmission. Like drift said, the teeth might not line up right when you go put it in to gear. But that's hardly a Prelude-only issue..... every manual tranny I've driven I've had to do that occasionally. There is nothing wrong, so long as you don't jamm 'em. The quickest and easiest way to line them up is to put it into neutral, clutch and put it in to any other gear, then back into first and it will slip right in.

Epoxy, if your tranny was replaced already, good chance the thing was beat up bad. If you don't treat it like a Kenworth 18 gear the tranny should last forever.