I have modified my TRD shifter 12 times to get to the point where the position, travel, weight and quietness is optimal for me.
Back when i put a B/M in my 350Z, they had a drawing of a corner of the assembly that you needed to file off before installing, in order to not pop out of 6th. Having said that, the aftermarket shifters (being shorter and all) sometimes pop out of gears or grind because of the geometry of it.
Here's what i would do: take out the whole shifter assembly, look down where the shifter goes in the gearbox and locate the little round hole where the shifter would sit in. Stick a 1/2 copper pipe in it, or something that's long enough for you to grab. Rock it back and forth with the engine off, to get a feel for which gear is what. Than sit on the passenger seat and get ready to shift. Have a buddy turn the engine on and as he clutches, you shift (figure out a communication pattern with him). If you get it up and down 1st and 2nd and it doesn't pop out, then your problem is the shifter, not the tranny (and i think it is). Try it, it won't cost you but a brew for your buddy...