How about draining the oil out of the trans? If you get some broken teeth or other parts, proceed with removal of the transmission. If the oil is clean, proceed with checling out the shift linkage. If everything seems to work correctly when you let out the clutch in second and third, but you get a terrable noise and the car will not move when you let out the clutch in first and reverse, it may well be in the transmission.
With the car at a stop and the engine running at idle, and the clutch pedal pushed all the way down, if the transmission will shift into second and third without making noise, but grinds when you try to shift into low or reverse, but the car moves in all gears, the clutch may not be fully releasing. Please understand, because first and reverse are not Syncronized, you may have to wait a few seconds with the clutch fully depressed to let everything in the trans to stop rotating before you can shift into low and reverse with out a little noise.
Just a suggestion,
Chris