Are Mods allowed in the FFG Tournaments? I ask because I want to add lights to my flotilla and still do tournaments. And maybe a few mag mounts.

As long as your modification doesn't make it so the ship can be confused with another ship, you should be all right. The TO of the tournament has the final say, but lights shouldn't be a problem.

You should be good:

Here's what I found from the X-Wing™ Tournament Regulations - Version 1.1.1 / Effective 08.01.2016

"Players are welcome and encouraged to personalize their squads according to the following rules:

• Players may paint their ship models. They cannot modify a ship model in any way that
would create confusion about which ship the model represents.

• Players cannot modify ship bases to alter their size or shape. Weight may be added to a ship
base if it does not alter the shape of the base. Ship pegs (including the connecting pegs
affixed to ship models) may be modified or replaced with a different connecting method."

Link:

https://www.fantasyflightgames.com/en/products/x-wing/?section=support#/support-section