I'm trying to find where the rules say you can only have one modification per ship. I have seen references to having two anti pursuit lasers on a ship and the shuttle comes with two. Is this not actually possible?

So for example are any of the following choices legal?

2xAnti Pursuit Lasers & 1xShield Upgrade

2xShield Upgrade

You may only have one modification card and one title card on a ship. Any of the ships that came with modification cards should have come with a rules card that covers how to use them. I tried to find a picture online but no one seems to have one. I have transcribed the full rules below:

Modifications and Titles

Reference Card

This card explains the rules for the Modification and Title cards. These Upgrade cards can be identified by their card backs.

Modifications and titles are special upgrades that do not appear in any ship's upgrade bar. Any ship may equip a modification or title unless the card is restricted to a specific type of ship. Each ship is limited to one modification and one title.

[Emphasis theirs.]

So, the Shuttle comes with TWO Anti-Pursuit Lasers not because the craft can have two, but because they give you an extra for use on other large ships if you were running both at the same time.

The rules for modifications are contained within the insert in any large ship rules insert.