What does the O&M cost/hr consist of?  Is it fuel cost/hr only or do we also add the regular maintenance cost/hr and top o/haul cost/hr to get the vale to insert in the generator input?

Don't include the fuel cost in the O&M cost.  You enter the fuel price separately, and HOMER tracks fuel usage and reports annual fuel cost.

Include everything else in the O&M cost: regular maintenance, minor overhauls, major overhauls, and any other hourly costs of operation.