You don't need to install v1 or v2 before installing v3. v3 has every ship from v1 and v2 aswell as improvments, making v1 and v2 redundent.
Which Prometheus (Star Trek ship) are you using? Please post a link to which prometheus mod it is.
You should have got the MVAM Prometheus (Star Trek ship) when installing MVAM Infinate as one of the requirements for v3 of the stargate ship pack. The script files for the MVAM Prometheus are independantly named so that they don't interfere with any other ship with Prometheus in its name.
Example:
MVAMPrometheus.py
MVAMPrometheusDorsal.py
MVAMPrometheusVentral.py
MVAMPrometheusSaucer.py