Regarding the gear shift linkage, make sure the shift lever moves up and down without hitting anything.  The shift from first to second gear may take a bit more lever movement since you must pass through neutral.  If the lever is bent or the linkage is out of adjustment, the travel might be limited.  The stop in the external gearshift mechanism should limit travel, not stuff like footpegs or the frame.  

After you make sure the gear shift linkage is in good working order and properly adjusted, I suggest you go through the "external gearshift mechanism" as outlined on pages 166 through 172 of the all inclusive Clymer manual.  Pay particular attention to the cam stopper (2) and it's associated spring (4).  If the spring is weak or broken, or the roller is heavily worn, the shift drum can rotate past the intended position and cause the gears to end up in between the desired position (like in between 2nd & 3rd rather than in 2nd).   Generally, a good indicator of stopper problems is difficulty finding neutral.  You having any trouble finding neutral?  Is your 2nd gear "grinding" issue only related to upshifts (i.e 1st to 2nd) or will it also occur on downshifts (i.e 3rd to 2nd)?