Mixed Physics and Custom Engine



First, I'm trying to create a game that would have extensive phisics simulation. By that i mean, objects that go flying, hit the walls, enemies, bounce, enemies fall, trip, ragdoll phisics, and more.
The thing is that there are certain simulation that i would prefer to design them myself without the physics engine properties. Is it feasible to integrate both a custom and physics objects?
By this i mean, creating objects that have physics enabled, that will rotate, fly, collide realistically, and other objects that will obey other custom coding. In fact, the problem here is that i need the latter to behave as physics in one state and without phisics in another state of the game.
Let me give you an example before i keep confusing you longer:
I want my character to control objects and make them fly around with her powers. When they are in the character's control, which means that they just follow the cursor, they will have some custom rotation, and a little motion done without the phisics engine. But then the character would be able to throw them, and that's when i need them to become phisics objects and behave as such, bouncing and pushing everything with force.

Second, if this is not possible then how difficult is to create a custom phisics engine for everything, that may not be as accurate as the GM one, but will achieve most of the things i need. Is there any tutorial or phisics custom code that i could read somewhere?

Thanks so much for reading everything!
Yes, using physics_pause_enable(true) to pause the physics simulation, and then you coding the other physics to become active using a check like

if (physics_pause_enable() = true) {
//your code here