I am unsure about project life time, fixed capital cost, fixed O&M cost, and capacity shortage penalty.

The project lifetime is simply the length of time over which you want to calculate the life cycle cost.  It is not an important variable, and I recommend leaving it at its default value of 25 years.

The system fixed capital cost is the capital cost of miscellaneous items (such as roads building) that are not accounted for in any of the component input windows.  You should not include the cost of the wind turbines in this value because you have already specified their cost in the Wind Turbine Inputs window.  I recommend you leave the system fixed capital cost at its default value of zero.

The system fixed O&M cost is the recurring annual cost of miscellaneous items (such as the labor cost of an annual site visit) that are not accounted for in any of the component input windows.  You have already accounted for the turbine O&M cost in the Wind Turbine Inputs window, so you should not include those costs here.  I recommend you leave the system fixed O&M cost at its default value of zero.

The capacity shortage penalty is an advanced input that you could use to assign a cost penalty to unmet load or capacity shortage.  There is no reason to use it in your analysis, so I recommend you leave the capacity shortage penalty at its default value of zero.