Regarding marker protocol

Hi,
I am using clinical gait data in .c3d format collected from BTS engineering system with 2 force plates.
I found that this data is not compatible with the Mocap model which is built in AMS,so i have made changes in the c3d file as per VICON marker system protocol .After the inverse dynamic analysis the output graphs are not matching the ideal nature of graphs

can anyone suggest me some solution for this issue and how to increase the step time.