Ben is giving you the correct answer.
Porting and polishing the ports is going to give you the most bang for the buck.
I would suggest sending the cylinders to Eric Gorr at forward Motion. He has been flow porting 2-strokes for decades and has it down to a science. http://www.eric-gorr.com/
Most air boxes are restrictive. This is done to hinder dirt, water and mud from entering the air box. If you open up your air box, you will allow the engine to breath better. Just don't get too carried away and pop rivet screens over any holes you make.
An after market silencer will also let the engine breath better. Pro Circuit and FMF both make after market non-spark arrested silencers.
The carbs will actually be a matter of choice. I like Bing, Keihin and Mikuni. I have actually had good performance out of of all of them. After the flow porting you can get away with a carbs that are 2-4mm larger than your stockers. If you go much larger than that, you will lose some low end grunt, but will gain it on the top end.
The cool head is only going to make a difference if you are racing in moto's that are over 20 minutes. If you are racing in motos that are over 20 minutes and you notice a decrease in horsepower, then and only then would I go for the aftermarket cool head.