The Mechanical Fatigue Tool (FT) directly uses the Mechanical calculated nodal stresses. It does not directly do IS0-4460 fatigue calculations. The FT has one general Fatigue Reduction Factor (Kf) that can be used to adjust the calculated stresses to include a reduction in resistance to fatigue damage for conditions such as surface finish. To include all the factors identified in IS-4460 in the FT calculations, you would need to determine the accumulated effect of all those factors and apply it as Kf. Also, some of the factors you identified (such as, size factor and endurance limit) are typically included by adjusting the S-N curve rather than the alternating.