I here people talking about no line,2 line, 3 line. On input shaft what dose that tell you and how do you check?  What is preferred? ...thanks

The input shaft has grooves in it, the number of grooves is how many 'lines' it has.  Each transmission has a different set of gear ratios.

Saginaw 3-speed 1st 2nd 3rd      
      No Lines (grooves)    2.85 1.68 1.00    
      1 Line    2.54 1.50 1.00      
      2 Lines  3.11  1.84  1.00      
      3 Lines   3.50  1.89 1.00      
Saginaw 4-speed 1st 2nd 3rd 4th  
       No lines 2.84 2.01 1.35 1.00  
       1 Line 2.54 1.80 1.44 1.00    
       2 Lines 3.11 2.20 1.47 1.00  
       3 Lines 3.50 2.47 1.65 1.00