I trade my 79' camaro for a 93' z28 with a 6 speed. When i got it ran fine and shifted good. The only problem was the clutch was slipping. The guy i got it from told me it need replaced. No big deal. a month or so after i bought it, the clutch finally went out. So as started to take the trans out i noticed that that between the gear box and housing at the end of the trans, where the shifter is, someone had put silicon around where they meet. i figure the silicon had gotten old and was leaking. i did have to put some trans fluid in it every once in a while. i got it out and cleaned it up. i pulled the end of the transmission off and put new silicon around it and started putting back together. i had gotten the bolts started and i had put the drive shaft in it just to make sure everything was lined up. i tighten the bolts up and it began to pull the rear part of the trans to the grear box. Right before it all came flush together THERE WAS A POP. i had no idea what happen. So i put it back in the car and hooked it all up except the drive shaft. i put the shifter on and fluid in the trans. When i got in the car to move the shifter around it would go to 1st thru 4th but it wouldnt go past 4th. so i have no 5th, 6th or reverse.The trans shifted fine when i got it so i know the grears arent out of it. What could have possibly happen?

 

That "POP" was most likely something cracking or breaking, and right then would have been a good time to take the shifter housing back off to take a look. You may not have had the 5-6 and/or reverse shifter rails lined up to the case, and bolting it together forced things till something had to give. I don't know if you could have gotten the 5-6 or reverse shift forks out of place and broke that when forcing the case parts back together, maybe. You need to open it back up and assess the damage, sure sounds like you broke something inside.