There's no restriction on how many Class permanents you can control, whether they're the same or different classes. Each Class permanent tracks its own level separately.

The resulting artifact creature will be able to attack on your turn if it's been under your control continuously since the turn began. That is, it doesn't matter how long it's been a creature, just how long it's been on the battlefield.

The artifact retains any types, subtypes, or supertypes it has.

An ability that advances a Class to a higher level is a normal activated ability. It uses the stack and can be responded to.

Gaining a level won't remove abilities that a Class had at a previous level.

If the target artifact has station, its base power and toughness will be set to 0/0. Adding charge counters to that artifact won't restore the power and toughness printed in any of its striations.

If the target artifact is an attached Equipment, it becomes unattached. If an Equipment without reconfigure becomes an artifact creature, it can't be attached to another creature.

If the target artifact is a Vehicle, its base power and toughness will be set to 0/0. Crewing that Vehicle will not restore its power and toughness.

Class cards have multiple text box sections. Other than the top section, each section contains a class level bar that includes a cost and a level number. Each represents an activated ability with the listed cost that advances the Class to the level listed in that bar.

Does Machines's level 3 ability doesn't remove any abilities the target artifact has.

Each Class starts at level 1 and has the abilities in the top section of its text box. Once a Class advances to level 2 or level 3, it has all of the abilities listed in the associated section of its text box as well.

You can't activate an ability that advances a Class to a particular level if that Class is already that level or higher. For example, if a Class is already level 2, you can't activate the ability that advances it to level 2 again.