First, measure the new shafts to make sure that you're not in posession of a smaller shaft... You can compare the old and the new, dry fit in the case...
I assemble the transmission with lube in various hard to reach places, but I leave the counter shaft and reverse shafts dry, don't lube the bearings- they'll be under oil soon enough... As you insert the shaft, use silicone on the last inch or so... Put a bit in the case on the other end. Drive shaft through, too far and put a bit in the case, and the second end of the shaft... Put the shaft in place, and before putting in the pin that holds the two shafts in place, fill the passage with silicone and push the pin through it. Clean up mess...
I've done this a couple of times and it's still working for me...
Karl