First Time Splitting Crankcase

So, I split my crankcase on my 1981 GPZ 550 in order to change the shift forks (shifting problems). I have come across a few things when putting it back together that I am hoping someone has the answers for.

1.) Should the secondary shaft require some force to be fitted back through the starter clutch. It goes through easily if I put the shaft through the backside (incorrect orientation) of the starter clutch from the right side of the case, but is giving some resistance when I try to put the secondary shaft through the correct side (side with the pins that has the gear fitted into it) coming from the right side of the case. 

2.) What direction do I rotate the shift drum to get to second gear? CW? CCW? I removed the neutral finder ball bearings and want to make sure it rotates in 2nd gear. With those removed it should theoretically behave like a bike without the neutral finder I assume from reading other posts, so would I be able to shift through all gears on the shift drum and rotate the transmission freely now in all gears or no? I removed them because one I do not prefer the neutral finder and two I removed them just in case sticking bearing balls were causing or adding to my shifting issues. 

3.) I am nervous as this is my first time disassembling/assembling a crankcase, I am wondering if anyone has any additional checks outside the FSM recommendations that I can do along the way to ensure proper function of parts installed. For example, the FSM says to put the shift drum in the neutral position and attempt to rotate the transmission when the lower crankcase is first refitted to the upper. Is there something similar I can do for the secondary shaft after I install it to ensure proper assembly? I do not believe the FSM says anything regarding that. 

Thank you in advance! 
-Travis

You should be able to shift through all the gears by spinning the clutch shaft if you removed the 2nd gear lock out ball bearings.

Okay, so I should be able to turn the shift drum into any gear if i just spin the clutch shaft? Do you know which direction to turn the shift drum for second?