Just remove it. You can pull the whole assembly or leave the valve on the transmission cover but its unnecessary after installing the exhaust.
I would go up a size from your jet and see how it runs. Earlier in the comments I mentioned I had a 72 jet in mine which was great for Atlanta using the Big Muff exhaust. I'd bet the jetting would be similar or same if I had the Tecnigas on instead. Your jetting may be different so I would go up a size and see how it runs first.
On your air box there should be a rubber hose on the back of the air box. At the end of that hose, some models had a plastic restrictor stuck in the end. It should be a 15mm x 12mm piece of plastic. I would remove that if you have one. The hose is part number 8 in this diagram.