The game was played with the 3rd Edition rules and the main modifications in the rules were to make the system faster to play since the original Ars Magica took place over years.
Also the weaponry has changed over the centuries so that firearms and other newer weapons had to be added.

Naturally all of these modifications are suggestions ...

Actions

As per the standard rules. New skills may need to be allowed to players since knowledge has moved on.

Use the duelling combat rules, since it fits in better with the style of the game.

Also there are some new rules for the use of firearms, these are detailed on the missile weapons sheet.

New Melee Weapons Table ...

New Missile Weapons Table ...

Magick The foci used by magi are becoming rarer as the fantastical creatures that might once have been killed for a part of their body rush towards extinction.

Given the game moves quicker than conventional Ars Magica I've found dropping the time required to make objects or do research from a season to a month of dedicated work is about right.

The new magick of the Followers of Thoth wasn't intended to be used by players - primarily because I haven't generated any rules for it. Basically their magick works by invoking fundamental aspects of the world around them. Normally this is done by a practioner who uses a hand painted set of tarot cards as a focus. The flavour of magick is basically invoked according to the card used.

While Tarot cards are still rare in many places they are gaining popularity amongst some of the nobility. The Followers of Thoth (one possible interpretation of tarot is Book of Thoth) spread it amongst them as a smokescreen for their own activities.

That's all of it. The rules modifications which were of course naturally ignored once the game really got going so chop and change as you feel appropriate!