No additional loop is necessary.
You can replace your existing loop with this one:
for t =1:p newmodVector1(t)=motData(t,1).*(motData(t,2)-(t<=2)); end
Or you can do it without a loop at all:
newmodVector1=(motData(:,1).*(motData(:,2)-((1:p).'<=2))).';
Omit the final transpose (.') if you want newmodVector1 to be a column vector.