Soooo, the problem is "marginally" better. But basically the same symptoms continue. I'm at a loss - it's only second gear and if it were truly popping out and back in, the shift fork would HAVE to be bent - but the old ones are not. I know it has to be something with the output shaft gears since the gears on the input shaft do not mesh dogs in second gear, but I cant imagine what the issue could be. I know it has to be the transmission because the one I swapped in a while back (before it lost a tooth) did not exhibit this problem whatsoever. Everything was quadruple checked with the manual before installing, so I'm confident it was not a fault of mine. Could it be that the dogs were worn short and are making a very poor connection in second, or could this be an output shaft tolerance/position issue?