I had a 2000 R1 and pulled that clutch cover more times than I care to remember. I always added a little oil to the top of that pin to help hold it out straight. It acts like a little glue if you know what I mean. The splines on that pin need to be pointing to the 2 o'clock direction, just a little off vertical. the lever on the housing needs to poiint away from the bike. As you slip on the cover, you've got to wiggle it to get the pin to sit inside it's hole. as you put on the cover the lever on the cover will get pulled in by the gears. If the cover is on and the lever can still be pulled by your hand, it's not right. Start all over.
It's not rocket science, but it is a pain in the ass. I haven't worked on that bike in over two years, so I might be wrong about the 2 o'clock position, but it's something like that. Good luck!