Congratulations, and welcome.
Yes, the problem gets better with miles. No, it never goes away.
The transmission is very rough, crude, especially in 1st and 2nd gear, but it has to be tough to take the torque.
The way I have learned to ride it, is to pull in the clutch, push the shifter down and HOLD PRESSURE on it, while you let out on the clutch just a little to make sure it engages. Most of the time it will be in gear, but if not completely in gear, it will THUNK and go in gear, and all is good.
Enjoy!!!