This is my first K bike and I did not even realize there was supposed to be boot cover until after I had posted.. . . I can shift the bike into gear by manually lifting the shift lever, but the rod itself is very stiff to move.
Hold on there, partner.
First, get a new clutch piston, clutch rod, spring and boot from
MaxBMW. You need three of those parts and could need the clutch rod to work with the new style piston, also. But first realize this. The gears are shifted by means of compound leverage. One of those levers is your foot pivoting on your ankle. The others are the foot shifter pivoting on its axle from the transmission and the clutch arm relieving pressure on the pressure plate by pressing on the diaphragm spring. Your shifting the rod manually can't match the eifficiency of those three items together, so shifting manually would be stiff regardless of the rod's condition. Order those items and install them first. You could remove the transmission, sure.
What are the sources of the instructions you followed? You missed some critical elements, as you now realize.