* If the individual particles have their mass increased does the gravitational force scale with it?
Yes, the gravitational force is dependent on mass, and will increase with denser (mass/volume) objects. Unless your character can affect mass values without restraint, he probably wont make objects heavy enough to have their own noticeable gravitational field (and if he did, wouldn't be good for the Earth).
* If something was given negative or zero mass, would that object cease to exist? Or at least be unable to be interacted with for all intents and purposes.
We don't really know. 'Negative mass' is part of theoretical physics. Perhaps it would produce antigravity? https://en.wikipedia.org/wiki/Negative_mass As for zero mass objects, they would essentially be weightless and have no gravitational field. They would travel at the speed of light.
* If the value of mass was increase for individual particles would it eventually become too much of a burden for the electromagnetic force holding the molecule's together or even the nuclear force holding the atoms themselves together?
No. At these scales the forces that hold them together are a lot stronger than the weights of the particles, which are then dependent on the gravity. The reason why large atoms fall apart is due to too much electrostatic repulsion, not because the atom is actually heavy. So no, changing the weight of fundamental particles would not result in some breakdown.
* If the value of mass changed what effects would it have on other values like charge, etc?
None. These values are pretty much independent of eachother. 343
We dont know why they even exist.
* If an Object at the center had it's mass decreased but on the outside layer had it's mass increased? Would the negative and positive mass cancel each other out for a net mass of 0 making the object light enough to carry. (Even if it's a large object like a car or piece of large furniture.) If you hit someone with this object would the person not feel any mass (0 mass) based off the total net mass of negative and positive mass or would they feel the outside layer of "positive mass" so the person holding the object could effectively be holding an object that weighs nothing but hit's like a truck when slammed against objects?
They would feel the mass hit them, but again, we dont know the true properties of negative mass. The object would be destroyed for all we know.
* Would the durability of an object scale up or down or remain the same with a mass change. (Ergo if a large object becomes light as a feather would it's durability scale so that if you grabbed it to lift it the pressure from your fingers would puncture it like what should happen when people with super strength lift most large objects in fiction.
No, it wouldnt. Durability depends on the bonds between atoms in the material, not the mass of the object. Gold is more massive than titanium, but titanium is more durable.
* If this person turned himself into negative mass or zero mass. (His entire person including the electric pulses in his nervous system.) Could he make at the speed of light(0 mass) or faster then light(negative mass) I've often heard that some people think that if you could have negative mass you could move faster then light. Would changing the mass value of an entire functioning human body have any negative effects of it's functioning?
Again, we have no idea whether negative mass is even possible. Zero mass would have you travelling at the speed of light however, but that will result in time not moving for the person, so they would probably end up dead by collision.
* If this person created a localized area of negative mass, could it behave like a vacuum until enough positive mass filled the area to "neutralize it?" Could this person used a controlled intricate area/volume of negative and positive mass to control, distribute, negate, increase, or shift the change in force, pressure, or acceleration in a certain area?
Impossible to know. Only looking for educated answers in this area won't achieve much. 781