You should get some more helpful answers if you told us what sort of car you want to build and what sort of track you want to run on.
for tuning, is there a best brand?
No one brand is best for everything.
What is best depends on what sort of car you want to build and what sort of track you want to run on.
Are you running on a home track or at a club? If at a club there are usually rules about what you can do, and more important there are winning cars to look at - the best starting point is to talk to the winners and see what they advise works at that club.
Somebody has already mentioned NSR and Slot.it - both excellent choices for some sorts of racing - not allowed at some clubs and way off the pace in others.
can you use motors from one company on any brand?
There are several standard sizes of motor.
You can swap the motors of the same size from any brand (providing there is a shaft at the right end for the pinion).
If you are scratch building a chassis you can use any motor.
More motor power isn't necessarily better, a chassis can only use so much power beyond which it becomes progressively more difficult to drive. An overpowered car isn't quicker, just more likely to crash!
i'm looking at totally modifying everything, motors, gears, tires ect and just wondering about the best option.
You haven't mentioned chassis, that can be one of the most important things.
wheres the best place to buy cars, more importantly, upgrades?
Depends what sort of cars and parts you want. There are some great mail order places like Pendle for the plastic chassis/ hard body cars and SCD for the metal chassis / soft body cars, you just need to clarify what section of market you are looking for.