Quick question: Can my players choose a Modified Cypra Drive using Planet bound for Millenia?

My initial reaction is yes.. if they use both the free modified drive and the bonus archeotech item to do it. The drive is already old... so why can't it be modified as well?

Taken directly from the Modified Drive entry:

The STC standard drive for this vessel is much older...

If this Archeotech is installed on a ship, apply its benefits to a standard plasma drive.

In both cases the term "standard drive" is used, lending credence to the interpretation that a non-Archeotech drive is meant here. However, the wording here is pretty loose as no actual RAW definition of a "standard drive" exists. As such, my reaction to that would be a no, but its up to you in the end.