No idea of the initial cost of the server, it has 5 year warrenty on it. in 5 years the school will be under BSF so who knows what will happens then.
1 - The server had an initial cost and even if you do not need to replace it you need to assign a value to it in case of a disaster and it needs to be replaced. Likewise if you have remaining hardware support on it that this has an associated cost that you have already paid out.
2 - Linux is free but may have support or training costs. If you have these in place now then you can justify further training when new versions of the OS come out. This could be courses or simply dedicated time for self-study.
3 - Public IP : already paid for but negligible really and the same cost whether you use OSS or other systems.
4 - Training : your time is money and is already paid for. Again, you need to include this in your costs because other VLE providers will include it in theirs and your costs (by the hour) are likely to work out cheaper anyway.
5 - Moodle : again, it is free but there are implications for development (themes and modules) and setup configuration. By including these in your model you cover all bases