1. Make sure the clutch is centered. This is not necessary if you didn't loosen the clutch.
2. Make sure the clutch rod is fully seated in the transmission. Loosen the clutch adjuster fully.
3. Make sure the transmission is not putting weight on the rod. Ideally, you should be using guide bolts on the transmission. At the very least, blocks or a jack should be used to keep it straight, as you slide it onto the splines. Once the spines are engaged, you are most of the way there.