Give it a good tune up. Make sure the stock air filter is fitted, clean and in good shape. Inspect and replace the plugs points and condensers as needed. Adjust your valves and cam chain along with your clutch and cable. Clean and lube all of your cables. Replace your front brake fluid after you install stainless steel lines,disassemble your front caliper and pivoting bracket so you lube the pivot point and inspect the piston and seal and pads replacing as needed. I would take this opportunity to deglaze the front disc, too. Replace your fork seals and fork oil. Replace your rear shocks. Check you wheel bearings, steering stem bearings swing arm bushings, chain and sprockets and rear brake shoes replace as needed. Then check all of your bulbs and adjustments.
Those are the best upgrades you can do and you won't know what you need until you do those things. As far as other upgrades, start with good tires, like the von Am26, Pirelli Sport Demon, Michelin MacAdam, Bridgestone BT 45 or S11, Dunlop GT501 or the Conti Attack. All are good to great tires, well suited to your bike. You may have noticed I haven't suggested other brands like Shinko or IRC or whatever. There is a reason. I would also change the bars to a set of superbike bars, not clubman or clip-ons. I would also consider a set of progressive suspension fork springs.
Once you have done all of these things at it and ridden iy for a thousand or so miles, come on back and ask a real question. Then we can talk about carbs and pipes and non-stock gearing and all kinds of other stuff that won't help it be a better running or riding bike.
